Variant report

Variant	rs666834
Chromosome Location	chr11:65183815-65183816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65183243..65184037-chr11:65193907..65194589,2	K562	blood:
2	chr11:65133537..65134417-chr11:65183554..65184219,2	MCF-7	breast:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65183635..65190622-chr11:65305653..65310980,8	MCF-7	breast:
5	chr11:65183627..65184422-chr11:65277909..65278800,2	MCF-7	breast:
6	chr11:65180960..65183956-chr11:65341785..65343462,2	MCF-7	breast:
7	chr11:65183475..65184491-chr11:65277927..65278879,6	K562	blood:
8	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
9	chr11:65183514..65184560-chr11:65199993..65201519,4	K562	blood:
10	chr11:65149440..65149947-chr11:65183096..65184005,2	K562	blood:
11	chr11:65183235..65184703-chr11:65235912..65236995,6	K562	blood:
12	chr11:65183121..65184524-chr11:65236045..65236987,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251562	Chromatin interaction
ENSG00000173727	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000162241	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11602839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[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];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239895	0.81[ASN][1000 genomes]
rs2904976	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]
rs3741384	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs475967	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs481335	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs508286	0.85[EUR][1000 genomes]
rs550015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs550894	0.82[EUR][1000 genomes]
rs573864	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs580933	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs61154080	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs673753	0.85[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs680413	1.00[CHB][hapmap];0.80[CHD][hapmap];0.80[ASN][1000 genomes]
rs7925823	0.91[CHB][hapmap]
rs7940559	0.85[LWK][hapmap];0.88[YRI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs666834	BANF1	cis	parietal	SCAN
rs666834	SLC22A25	cis	cerebellum	SCAN
rs666834	POLA2	cis	parietal	SCAN
rs666834	SLC22A11	cis	parietal	SCAN
rs666834	PPP6R3	cis	cerebellum	SCAN
rs666834	PLCB3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65171200-65184200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:65177600-65185400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65179800-65184000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:65181400-65189400	Weak transcription	Ovary	ovary
5	chr11:65181600-65184400	Weak transcription	Aorta	Aorta
6	chr11:65182200-65184000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:65182200-65189600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr11:65182400-65186200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:65182400-65188600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr11:65182800-65185800	Flanking Active TSS	HepG2	liver
11	chr11:65183000-65185600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:65183000-65186000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:65183000-65189200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:65183000-65189400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:65183200-65184000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:65183200-65185200	Enhancers	Gastric	stomach
17	chr11:65183200-65186800	Enhancers	Fetal Brain Male	brain
18	chr11:65183200-65186800	Enhancers	Fetal Heart	heart
19	chr11:65183200-65187200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:65183200-65188000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:65183400-65184000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr11:65183400-65184000	Enhancers	Fetal Thymus	thymus
23	chr11:65183400-65184000	Enhancers	Small Intestine	intestine
24	chr11:65183400-65184400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr11:65183400-65184800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:65183400-65184800	Enhancers	Pancreas	Pancrea
27	chr11:65183400-65184800	Enhancers	Spleen	Spleen
28	chr11:65183400-65185800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr11:65183400-65186000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:65183400-65186000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:65183400-65186000	Enhancers	Stomach Mucosa	stomach
32	chr11:65183400-65186000	Enhancers	HUVEC	blood vessel
33	chr11:65183400-65186200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:65183400-65186200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr11:65183400-65188600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:65183400-65188600	Flanking Active TSS	Hela-S3	cervix
37	chr11:65183400-65189200	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr11:65183400-65189200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr11:65183400-65189400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:65183400-65189400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr11:65183400-65189600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr11:65183400-65189600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:65183400-65190200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:65183600-65184000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr11:65183600-65184000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr11:65183600-65184000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr11:65183600-65184000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr11:65183600-65184000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr11:65183600-65184200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:65183600-65184200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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