Variant report

Variant	rs56211149
Chromosome Location	chr2:11485231-11485232
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	EP300	chr2:11484623-11485904	K562	blood:	n/a	chr2:11485239-11485248
2	CHD2	chr2:11484906-11485631	HepG2	liver:	n/a	n/a
3	IRF1	chr2:11484565-11485403	K562	blood:	n/a	n/a
4	CHD2	chr2:11485214-11485720	H1-hESC	embryonic stem cell:	n/a	n/a
5	ETS1	chr2:11485048-11485381	K562	blood:	n/a	n/a
6	POLR2A	chr2:11483664-11485408	HEK293	kidney:	n/a	n/a
7	POLR2A	chr2:11484391-11485980	PANC-1	pancreas:	n/a	n/a
8	JUND	chr2:11484750-11485505	A549	lung:	n/a	chr2:11485174-11485185
9	FOSL1	chr2:11484923-11485441	K562	blood:	n/a	chr2:11485174-11485185
10	MAZ	chr2:11482527-11485966	IMR90	lung:	n/a	chr2:11484107-11484117
11	JUND	chr2:11484941-11485398	H1-hESC	embryonic stem cell:	n/a	chr2:11485174-11485185
12	MAX	chr2:11483578-11485610	ECC-1	luminal epithelium:	n/a	chr2:11484107-11484117
13	TEAD4	chr2:11484961-11485737	K562	blood:	n/a	n/a
14	FOS	chr2:11485010-11485349	MCF10A-Er-Src	breast:	n/a	n/a
15	CHD2	chr2:11483659-11485828	Hela-S3	cervix:	n/a	chr2:11484574-11484584
16	POLR2A	chr2:11484471-11485423	GM10847	blood:	n/a	n/a
17	TBL1XR1	chr2:11484940-11485291	K562	blood:	n/a	n/a
18	CTCF	chr2:11485181-11485375	IMR90	lung:	n/a	chr2:11485245-11485258
19	CTCF	chr2:11485100-11485250	GM12871	blood:	n/a	n/a
20	POLR2A	chr2:11483825-11485635	HUVEC	blood vessel:	n/a	n/a
21	PAX5	chr2:11483927-11485368	GM12892	blood:	n/a	chr2:11484560-11484587
22	CTCF	chr2:11485200-11485350	AG09319	gingival:	n/a	chr2:11485245-11485258
23	SIN3AK20	chr2:11483595-11485509	PANC-1	pancreas:	n/a	n/a
24	TEAD4	chr2:11484861-11485866	A549	lung:	n/a	n/a
25	MAX	chr2:11482548-11486084	A549	lung:	n/a	chr2:11484107-11484117
26	BACH1	chr2:11484900-11485494	H1-hESC	embryonic stem cell:	n/a	n/a
27	ATF3	chr2:11484986-11485350	HepG2	liver:	n/a	chr2:11485045-11485054
28	MXI1	chr2:11481913-11486311	SK-N-SH	brain:	n/a	n/a
29	MAX	chr2:11482699-11485758	HepG2	liver:	n/a	chr2:11484107-11484117
30	POLR2A	chr2:11483555-11485468	H1-neurons	neurons:	n/a	n/a
31	FOS	chr2:11484993-11485340	MCF10A-Er-Src	breast:	n/a	n/a
32	RXRA	chr2:11484652-11485739	HepG2	liver:	n/a	chr2:11485242-11485262
33	EGR1	chr2:11485039-11485373	K562	blood:	n/a	chr2:11485048-11485061 chr2:11485318-11485329
34	MYC	chr2:11483622-11485498	K562	blood:	n/a	chr2:11484107-11484117
35	TEAD4	chr2:11484822-11485767	A549	lung:	n/a	n/a
36	BRCA1	chr2:11484901-11485468	HepG2	liver:	n/a	n/a
37	JUND	chr2:11484778-11485335	H1-hESC	embryonic stem cell:	n/a	chr2:11485174-11485185
38	POLR2A	chr2:11482729-11486472	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr2:11484566-11485845	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:11484494-11485917	K562	blood:	n/a	n/a
41	MAZ	chr2:11482539-11485760	HepG2	liver:	n/a	chr2:11484107-11484117
42	POLR2A	chr2:11482788-11486262	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr2:11482618-11486449	Hela-S3	cervix:	n/a	n/a
44	CHD2	chr2:11484850-11485730	K562	blood:	n/a	n/a
45	ATF3	chr2:11485057-11485293	K562	blood:	n/a	n/a
46	TEAD4	chr2:11484941-11486000	HCT-116	colon:	n/a	n/a
47	TCF7L2	chr2:11485019-11485816	Hela-S3	cervix:	n/a	n/a
48	GABPA	chr2:11484728-11485305	K562	blood:	n/a	chr2:11485239-11485248
49	CTCF	chr2:11485180-11485330	GM12864	blood:	n/a	chr2:11485245-11485258
50	MBD4	chr2:11484737-11485900	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11446328..11449302-chr2:11482839..11485533,2	MCF-7	breast:
2	chr2:11482372..11487550-chr2:11525654..11531960,9	MCF-7	breast:
3	chr2:11373041..11376680-chr2:11481459..11486793,6	MCF-7	breast:
4	chr2:11481545..11486787-chr2:11491378..11496218,8	MCF-7	breast:
5	chr2:11483291..11485571-chr2:11604286..11606431,2	MCF-7	breast:
6	chr17:27620648..27621777-chr2:11484781..11485516,3	NB4	blood:
7	chr2:11483940..11486207-chr2:11530235..11532034,2	K562	blood:
8	chr11:17229956..17230914-chr2:11484768..11485358,2	Hela-S3	cervix:
9	chr2:11292941..11297094-chr2:11480820..11486254,6	MCF-7	breast:
10	chr2:11484521..11487208-chr2:11489833..11492072,2	K562	blood:
11	chr2:11483049..11486978-chr2:11530307..11533471,4	MCF-7	breast:
12	chr2:11482371..11485428-chr2:11534025..11537515,3	K562	blood:
13	chr2:11484922..11486828-chr2:11507256..11509884,2	K562	blood:
14	chr2:10951194..10953015-chr2:11483398..11486312,2	MCF-7	breast:
15	chr2:11484673..11485608-chr6:30584791..30585452,2	Hela-S3	cervix:
16	chr2:11482684..11486384-chr2:11678704..11682899,6	MCF-7	breast:
17	chr2:11485129..11485840-chr2:68479649..68480177,2	Hela-S3	cervix:
18	chr2:11484880..11486405-chr2:11487822..11489457,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PQLC3-1	chr2:11485211-11485815	XLOC_001349
2	lnc-PQLC3-1	chr2:11485102-11485815	NONHSAT069160

Variant related genes	Relation type
ROCK2	TF binding region
ENSG00000143870	Chromatin interaction
ENSG00000224177	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000226961	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000221823	Chromatin interaction
ENSG00000207267	Chromatin interaction
ENSG00000108256	Chromatin interaction
ENSG00000230154	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000231403	Chromatin interaction
ENSG00000273064	Chromatin interaction
ENSG00000169016	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10198045	0.88[ASN][1000 genomes]
rs10754958	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11693061	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12468344	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4302194	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56309145	0.89[ASN][1000 genomes]
rs59048275	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	esv3449527	chr2:11483801-11486049	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56211149	ENSG00000134318	cis	multi-tissue	Pritchard
rs56211149	PQLC3	cis	Thyroid	GTEx
rs56211149	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs56211149	PQLC3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11479800-11485400	Active TSS	GM12878-XiMat	blood
2	chr2:11480000-11485800	Active TSS	Aorta	Aorta
3	chr2:11481000-11485600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:11481000-11485600	Active TSS	NHLF	lung
5	chr2:11481000-11485800	Active TSS	Ovary	ovary
6	chr2:11481200-11485600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:11481600-11485400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:11481600-11485400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:11481600-11485600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr2:11481600-11485600	Active TSS	Brain Germinal Matrix	brain
11	chr2:11481600-11485800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:11481800-11485600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:11481800-11485600	Active TSS	Fetal Intestine Large	intestine
14	chr2:11481800-11485600	Active TSS	NHDF-Ad	bronchial
15	chr2:11481800-11485800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:11481800-11486000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:11482000-11485400	Active TSS	A549	lung
18	chr2:11482000-11485400	Active TSS	Hela-S3	cervix
19	chr2:11482000-11485800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:11482000-11486000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:11482000-11486000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:11482200-11485400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr2:11482200-11485400	Active TSS	Colon Smooth Muscle	Colon
24	chr2:11482200-11485400	Active TSS	HSMMtube	muscle
25	chr2:11482200-11485600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:11482200-11485600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:11482200-11485600	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:11482200-11485800	Active TSS	Fetal Muscle Trunk	muscle
29	chr2:11482200-11485800	Active TSS	Psoas Muscle	Psoas
30	chr2:11482400-11485400	Active TSS	Fetal Muscle Leg	muscle
31	chr2:11482400-11485400	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:11482400-11485400	Active TSS	HSMM	muscle
33	chr2:11482400-11485600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:11482400-11485600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:11482400-11485600	Active TSS	Brain Anterior Caudate	brain
36	chr2:11482400-11485600	Active TSS	Fetal Intestine Small	intestine
37	chr2:11482400-11485600	Active TSS	Fetal Stomach	stomach
38	chr2:11482400-11485600	Active TSS	Left Ventricle	heart
39	chr2:11482400-11486400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr2:11482600-11485600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:11482600-11485600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:11482600-11485800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:11482600-11485800	Active TSS	Right Ventricle	heart
44	chr2:11482600-11486000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr2:11482600-11486000	Active TSS	Fetal Kidney	kidney
46	chr2:11482800-11485400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:11482800-11485400	Active TSS	Gastric	stomach
48	chr2:11482800-11485400	Active TSS	Lung	lung
49	chr2:11482800-11485400	Active TSS	Stomach Mucosa	stomach
50	chr2:11482800-11485600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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