Variant report

Variant	rs2904976
Chromosome Location	chr11:65185387-65185388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr11:65183014-65218224	IMR90	lung:	n/a	chr11:65189696-65189706 chr11:65213009-65213016
2	POLR2A	chr11:65185159-65185825	HepG2	liver:	n/a	n/a
3	CREB1	chr11:65185063-65185587	A549	lung:	n/a	n/a
4	POLR2A	chr11:65182982-65199920	Hela-S3	cervix:	n/a	n/a
5	SPI1	chr11:65184424-65185387	GM12878	blood:	n/a	chr11:65184951-65184960 chr11:65184495-65184508 chr11:65184952-65184959 chr11:65184949-65184962
6	NR2F2	chr11:65185235-65188013	K562	blood:	n/a	chr11:65186278-65186293
7	TFAP2C	chr11:65185329-65187138	Hela-S3	cervix:	n/a	chr11:65185967-65185982
8	STAT5A	chr11:65185338-65185902	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65184755-65189855	GM12892	blood:	n/a	n/a
10	POLR2A	chr11:65185349-65185583	A549	lung:	n/a	n/a
11	POLR2A	chr11:65184720-65188024	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:65184966-65198365	GM12892	blood:	n/a	n/a
13	MAZ	chr11:65184888-65186930	GM12878	blood:	n/a	chr11:65186027-65186037 chr11:65186307-65186316 chr11:65186579-65186588 chr11:65185478-65185488
14	EBF1	chr11:65185275-65185683	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:65184781-65187887	GM18505	blood:	n/a	n/a
16	EBF1	chr11:65185361-65185685	GM12878	blood:	n/a	n/a
17	NR3C1	chr11:65184956-65185797	A549	lung:	n/a	chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185417-65185431 chr11:65185417-65185431 chr11:65185416-65185432 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185413-65185434 chr11:65185322-65185335 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185416-65185432
18	POLR2A	chr11:65185268-65187802	GM15510	blood:	n/a	n/a
19	CHD2	chr11:65184917-65185512	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:65184905-65188006	ECC-1	luminal epithelium:	n/a	n/a
21	NFATC1	chr11:65185274-65185827	GM12878	blood:	n/a	n/a
22	SIN3A	chr11:65185307-65185433	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:65184788-65185816	A549	lung:	n/a	n/a
24	POLR2A	chr11:65185157-65185824	A549	lung:	n/a	n/a
25	POLR2A	chr11:65185091-65185828	A549	lung:	n/a	n/a
26	STAT5A	chr11:65184377-65187873	GM12878	blood:	n/a	chr11:65184533-65184545
27	POLR2A	chr11:65184867-65198324	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:65182298-65198746	GM12878	blood:	n/a	n/a
29	REST	chr11:65185172-65185769	A549	lung:	n/a	chr11:65185304-65185317
30	RUNX3	chr11:65184453-65187292	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:65184718-65196445	HL-60	blood:	n/a	n/a
32	POLR2A	chr11:65184629-65187242	GM12878	blood:	n/a	n/a
33	POLR2A	chr11:65185191-65187825	GM18951	blood:	n/a	n/a
34	NR3C1	chr11:65185192-65185588	A549	lung:	n/a	chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185417-65185431 chr11:65185417-65185431 chr11:65185416-65185432 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185413-65185434 chr11:65185322-65185335 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185416-65185432
35	ELF1	chr11:65184432-65187191	GM12878	blood:	n/a	chr11:65184475-65184487 chr11:65184948-65184961
36	POLR2A	chr11:65178313-65199265	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr11:65184926-65198709	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:65185328-65185684	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr11:65184750-65188037	GM12891	blood:	n/a	n/a
40	NR3C1	chr11:65185179-65185579	A549	lung:	n/a	chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185417-65185431 chr11:65185417-65185431 chr11:65185416-65185432 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185413-65185434 chr11:65185322-65185335 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185416-65185432
41	POLR2A	chr11:65185363-65185494	IMR90	lung:	n/a	n/a
42	EP300	chr11:65185372-65185593	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:65185129-65187045	ProgFib	skin:	n/a	n/a
44	POLR2A	chr11:65184830-65187794	GM12892	blood:	n/a	n/a
45	NR3C1	chr11:65185101-65185584	A549	lung:	n/a	chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185417-65185431 chr11:65185417-65185431 chr11:65185416-65185432 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185413-65185434 chr11:65185322-65185335 chr11:65185416-65185432 chr11:65185411-65185437 chr11:65185411-65185437 chr11:65185416-65185432
46	MTA3	chr11:65182457-65199360	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:65185221-65186930	MCF-7	breast:	n/a	n/a
48	POLR2A	chr11:65184993-65198340	K562	blood:	n/a	n/a
49	POLR2A	chr11:65185330-65196319	GM12878	blood:	n/a	n/a
50	BCLAF1	chr11:65185306-65185849	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65058175..65060468-chr11:65184473..65187449,2	MCF-7	breast:
2	chr11:65184946..65185560-chr11:65277651..65278446,2	K562	blood:
3	chr11:65184438..65186066-chr11:65627454..65629412,2	K562	blood:
4	chr11:65095990..65098961-chr11:65184983..65186662,2	K562	blood:
5	chr11:65185354..65186080-chr20:48329946..48330569,2	Hela-S3	cervix:
6	chr11:65184878..65185776-chr11:65194577..65195444,2	K562	blood:
7	chr11:65185377..65188145-chr9:37488495..37490898,2	K562	blood:
8	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
9	chr11:65183635..65190622-chr11:65305653..65310980,8	MCF-7	breast:
10	chr11:65184392..65191686-chr11:65339528..65345365,10	K562	blood:
11	chr11:65184078..65185809-chr13:58455103..58457329,2	MCF-7	breast:
12	chr11:65184042..65186636-chr11:65381188..65384073,2	K562	blood:
13	chr11:65184371..65196984-chr11:65316952..65328208,29	K562	blood:
14	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
15	chr11:65185186..65203592-chr11:65286522..65299399,55	K562	blood:

Variant related genes	Relation type
NEAT1	TF binding region
ENSG00000173327	Chromatin interaction
ENSG00000173727	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000158470	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000230188	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000176973	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11602839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605125	0.85[CEU][hapmap]
rs2073801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741384	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs475967	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs481335	0.88[EUR][1000 genomes]
rs508286	0.85[EUR][1000 genomes]
rs550015	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs550894	0.82[EUR][1000 genomes]
rs573864	0.90[CHB][hapmap]
rs580933	0.85[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs61154080	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs673753	0.85[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs680413	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs7925823	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2904976	SLC22A25	cis	cerebellum	SCAN
rs2904976	POLA2	cis	parietal	SCAN
rs2904976	SLC22A11	cis	parietal	SCAN
rs2904976	PLCB3	cis	cerebellum	SCAN
rs2904976	PPP6R3	cis	cerebellum	SCAN
rs2904976	NEAT1	cis	Muscle Skeletal	GTEx
rs2904976	BANF1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65177600-65185400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:65181400-65189400	Weak transcription	Ovary	ovary
3	chr11:65182200-65189600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr11:65182400-65186200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:65182400-65188600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr11:65182800-65185800	Flanking Active TSS	HepG2	liver
7	chr11:65183000-65185600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:65183000-65186000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:65183000-65189200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:65183000-65189400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:65183200-65186800	Enhancers	Fetal Brain Male	brain
12	chr11:65183200-65186800	Enhancers	Fetal Heart	heart
13	chr11:65183200-65187200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:65183200-65188000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:65183400-65185800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr11:65183400-65186000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:65183400-65186000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:65183400-65186000	Enhancers	Stomach Mucosa	stomach
19	chr11:65183400-65186000	Enhancers	HUVEC	blood vessel
20	chr11:65183400-65186200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:65183400-65186200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr11:65183400-65188600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:65183400-65188600	Flanking Active TSS	Hela-S3	cervix
24	chr11:65183400-65189200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr11:65183400-65189200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr11:65183400-65189400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr11:65183400-65189400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr11:65183400-65189600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr11:65183400-65189600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:65183400-65190200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:65183600-65185600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:65183600-65185600	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr11:65183600-65185800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:65183600-65185800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr11:65183600-65185800	Flanking Active TSS	Esophagus	oesophagus
36	chr11:65183600-65186000	Enhancers	Fetal Lung	lung
37	chr11:65183600-65186200	Flanking Active TSS	A549	lung
38	chr11:65183600-65186600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr11:65183600-65187400	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr11:65183600-65188000	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr11:65183600-65188000	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr11:65183600-65188600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr11:65183600-65188600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr11:65183600-65188600	Flanking Active TSS	Colonic Mucosa	Colon
45	chr11:65183600-65188600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr11:65183600-65189000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:65183600-65189200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:65183600-65189400	Flanking Active TSS	GM12878-XiMat	blood
49	chr11:65183600-65189600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr11:65183600-65189600	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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