Variant report

Variant	rs2576722
Chromosome Location	chr2:55461823-55461824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
2	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
4	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:55459010-55461927	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
7	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
10	MBD4	chr2:55458795-55461839	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
15	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
16	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:55461692-55462150	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr2:55461421-55462031	U87	brain:	n/a	n/a
19	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
20	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
23	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
24	ZNF263	chr2:55459016-55461900	HEK293-T-REx	kidney:	n/a	n/a
25	POLR2A	chr2:55461775-55462109	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:55458733-55465490	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:55461687-55462658	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr2:55461784-55462017	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:55458865-55465521	MCF-7	breast:	n/a	n/a
30	POLR2A	chr2:55460323-55464639	A549	lung:	n/a	n/a
31	POLR2A	chr2:55458817-55464677	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:55461565-55464760	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr2:55458685-55467019	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr2:55459009-55464639	GM12892	blood:	n/a	n/a
35	POLR2A	chr2:55459696-55465435	K562	blood:	n/a	n/a
36	POLR2A	chr2:55461263-55461827	HL-60	blood:	n/a	n/a
37	POLR2A	chr2:55458747-55464854	U87	brain:	n/a	n/a
38	BCL3	chr2:55461606-55462520	A549	lung:	n/a	n/a
39	POLR2A	chr2:55461332-55462156	GM12891	blood:	n/a	n/a
40	POLR2A	chr2:55461740-55462209	GM12891	blood:	n/a	n/a
41	POLR2A	chr2:55460860-55462031	U87	brain:	n/a	n/a
42	ATF2	chr2:55461348-55461866	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr2:55458947-55464599	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:55461354-55464525	GM12891	blood:	n/a	n/a
45	POLR2A	chr2:55458451-55467274	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr2:55461307-55462005	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr2:55458733-55464641	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:55461538-55464657	GM12892	blood:	n/a	n/a
49	POLR2A	chr2:55461478-55464741	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr2:55458884-55465602	PFSK-1	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
2	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
3	chr17:57919487..57921628-chr2:55460501..55462131,2	MCF-7	breast:
4	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
5	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
6	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:

No data

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17046778	0.83[ASN][1000 genomes]
rs1821832	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589092	0.81[CHB][hapmap]
rs57681837	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59439819	0.83[AMR][1000 genomes]
rs59783675	0.81[AMR][1000 genomes]
rs61109509	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6726380	0.83[ASN][1000 genomes]
rs7349360	0.83[AMR][1000 genomes]
rs7349405	0.90[CHB][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2576722	CLHC1	cis	Whole Blood	GTEx
rs2576722	CLHC1	cis	Artery Tibial	GTEx
rs2576722	CLHC1	cis	Artery Aorta	GTEx
rs2576722	CLHC1	cis	Adipose Subcutaneous	GTEx
rs2576722	C2orf63	cis	Lymphoblastoid	GTEx
rs2576722	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs2576722	FLJ31438	cis	multi-tissue	Pritchard
rs2576722	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55458600-55462200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55459800-55462000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr2:55460000-55462400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
4	chr2:55460000-55463000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
5	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
6	chr2:55460200-55462000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
7	chr2:55460200-55462200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:55460200-55462600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr2:55460200-55463000	Transcr. at gene 5' and 3'	A549	lung
10	chr2:55460400-55462000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
11	chr2:55460400-55462000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
13	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Hela-S3	cervix
14	chr2:55460400-55462600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
15	chr2:55460400-55462600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:55460400-55463000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:55460600-55462000	Transcr. at gene 5' and 3'	Osteobl	bone
18	chr2:55460600-55462200	Transcr. at gene 5' and 3'	NH-A	brain
19	chr2:55460600-55462400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr2:55460600-55462600	Weak transcription	Aorta	Aorta
21	chr2:55460600-55463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
23	chr2:55460800-55462000	Transcr. at gene 5' and 3'	HMEC	breast
24	chr2:55460800-55462200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:55460800-55462600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
26	chr2:55460800-55462600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
27	chr2:55461000-55462200	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr2:55461000-55462200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:55461000-55462400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:55461000-55462400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:55461000-55462400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:55461000-55462400	Genic enhancers	Brain Hippocampus Middle	brain
33	chr2:55461000-55462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:55461000-55462800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr2:55461000-55463000	Genic enhancers	Brain Germinal Matrix	brain
36	chr2:55461000-55463000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr2:55461000-55464600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:55461200-55462000	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:55461200-55462000	Genic enhancers	Primary B cells from cord blood	blood
41	chr2:55461200-55462000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:55461200-55462000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:55461200-55462400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:55461200-55462400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:55461200-55462400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:55461200-55462400	Genic enhancers	Brain Cingulate Gyrus	brain
47	chr2:55461200-55462400	Genic enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:55461200-55462600	Genic enhancers	NHDF-Ad	bronchial
49	chr2:55461200-55462800	Weak transcription	Pancreas	Pancrea
50	chr2:55461200-55463000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood

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