Variant report

Variant	rs1062292
Chromosome Location	chr2:20648211-20648212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:61)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:20646048-20648294	A549	lung:	n/a	chr2:20646693-20646703
2	MAX	chr2:20646207-20648216	A549	lung:	n/a	chr2:20646693-20646703
3	POLR2A	chr2:20646405-20648265	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:20646248-20649093	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr2:20646244-20650963	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:20646309-20648305	MCF-7	breast:	n/a	n/a
7	POLR2A	chr2:20646681-20651477	A549	lung:	n/a	n/a
8	MAFK	chr2:20647808-20651095	Hela-S3	cervix:	n/a	chr2:20650104-20650114 chr2:20650108-20650119 chr2:20650107-20650118 chr2:20650107-20650118 chr2:20650103-20650118 chr2:20650105-20650114 chr2:20650106-20650120 chr2:20650103-20650119
9	POLR2A	chr2:20646043-20652533	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr2:20646266-20651620	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr2:20646347-20648611	HUVEC	blood vessel:	n/a	n/a
12	RCOR1	chr2:20646392-20650844	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:20646356-20648978	Hela-S3	cervix:	n/a	n/a
14	PML	chr2:20647499-20648347	MCF-7	breast:	n/a	n/a
15	POLR2A	chr2:20645918-20651649	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr2:20646294-20651502	MCF-7	breast:	n/a	n/a
17	HEY1	chr2:20645541-20650862	HepG2	liver:	n/a	chr2:20646608-20646623
18	MYBL2	chr2:20646154-20651084	HepG2	liver:	n/a	n/a
19	MAZ	chr2:20647679-20648219	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:20646006-20652601	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:20645948-20651806	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr2:20645989-20652401	IMR90	lung:	n/a	n/a
23	SIN3AK20	chr2:20646159-20648886	MCF-7	breast:	n/a	n/a
24	SP1	chr2:20647905-20649064	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAZ	chr2:20646022-20649127	IMR90	lung:	n/a	chr2:20646693-20646703
26	POLR2A	chr2:20646359-20648760	ProgFib	skin:	n/a	n/a
27	MBD4	chr2:20646527-20651011	HepG2	liver:	n/a	n/a
28	MAZ	chr2:20646438-20648591	Hela-S3	cervix:	n/a	chr2:20646693-20646703
29	JUND	chr2:20646497-20648227	HepG2	liver:	n/a	chr2:20646719-20646728
30	RFX5	chr2:20647965-20648600	HepG2	liver:	n/a	n/a
31	MAX	chr2:20646550-20648875	HepG2	liver:	n/a	chr2:20646693-20646703
32	POLR2A	chr2:20646427-20648270	A549	lung:	n/a	n/a
33	MXI1	chr2:20646507-20648967	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:20647758-20648934	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr2:20645976-20650968	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:20646414-20649055	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:20646257-20649015	GM12892	blood:	n/a	n/a
38	ZNF263	chr2:20646564-20648990	HEK293-T-REx	kidney:	n/a	n/a
39	POLR2A	chr2:20645826-20652982	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr2:20645973-20651501	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:20646438-20648772	GM12892	blood:	n/a	n/a
42	SMARCB1	chr2:20646128-20648648	Hela-S3	cervix:	n/a	n/a
43	ZKSCAN1	chr2:20646420-20648437	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:20648117-20648263	A549	lung:	n/a	n/a
45	RCOR1	chr2:20647581-20648666	Hela-S3	cervix:	n/a	n/a
46	CHD2	chr2:20646258-20650947	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:20646139-20648250	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr2:20646393-20648962	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:20646455-20650954	HepG2	liver:	n/a	n/a
50	CHD1	chr2:20645950-20651592	IMR90	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20648194-20648244	HCT-116	colon:	n/a
2	chr2:20648194-20648244	ECC-1	luminal epithelium:	n/a
3	chr2:20648194-20648244	HRE	kidney:	n/a
4	chr2:20648194-20648244	NHDF-neo	bronchial:	n/a
5	chr2:20648194-20648244	SAEC	small airway:	n/a
6	chr2:20648194-20648244	GM12878	blood:	n/a
7	chr2:20648194-20648244	BE2_C	brain:	n/a
8	chr2:20648194-20648244	SK-N-SH_RA	brain:	n/a
9	chr2:20648194-20648244	SKMC	muscle:	n/a
10	chr2:20648194-20648244	GM06990	blood:	n/a
11	chr2:20648194-20648244	AG04449	skin:	fetal
12	chr2:20648194-20648244	GM19239	blood:	n/a
13	chr2:20648194-20648244	K562	blood:	n/a
14	chr2:20648194-20648244	HIPEpiC	eye:	n/a
15	chr2:20648194-20648244	PrEC	prostate:	n/a
16	chr2:20648194-20648244	LNCaP	prostate:	n/a
17	chr2:20648194-20648244	CMK	blood:	n/a
18	chr2:20648194-20648244	HCM	heart:	n/a
19	chr2:20648194-20648244	HUVEC	blood vessel:	n/a
20	chr2:20648194-20648244	ovcar-3	ovarian:	n/a
21	chr2:20648194-20648244	Jurkat	blood:	n/a
22	chr2:20648194-20648244	Hela-S3	cervix:	n/a
23	chr2:20648194-20648244	HepG2	liver:	n/a
24	chr2:20648194-20648244	A549	lung:	n/a
25	chr2:20648194-20648244	H1-hESC	embryonic stem cell:	embryo
26	chr2:20648194-20648244	NB4	blood:	n/a
27	chr2:20648194-20648244	HMEC	breast:	n/a
28	chr2:20648194-20648244	HEEpiC	esophagus:	n/a
29	chr2:20648194-20648244	ProgFib	skin:	n/a
30	chr2:20648194-20648244	GM12891	blood:	n/a
31	chr2:20648194-20648244	HCF	heart:	n/a
32	chr2:20648194-20648244	MCF-7	breast:	n/a
33	chr2:20648194-20648244	IMR90	lung:	fetal
34	chr2:20648194-20648244	HL-60	blood:	n/a
35	chr2:20648194-20648244	BJ	skin:	n/a
36	chr2:20648194-20648244	Hepatocyte	liver:	n/a
37	chr2:20648194-20648244	HEK293	kidney:	embryo
38	chr2:20648194-20648244	HRCEpiC	kidney:	n/a
39	chr2:20648194-20648244	U87	brain:	n/a
40	chr2:20648194-20648244	HCPEpiC	choroid plexus:	n/a
41	chr2:20648194-20648244	Caco-2	colon:	n/a
42	chr2:20648194-20648244	HNPCEpiC	eye:	n/a
43	chr2:20648194-20648244	PANC-1	pancreas:	n/a
44	chr2:20648194-20648244	AG04450	lung:	fetal
45	chr2:20648194-20648244	HRPEpiC	eye:	n/a
46	chr2:20648194-20648244	RPTEC	kidney:	n/a
47	chr2:20648194-20648244	MCF10A-Er-Src	breast:	n/a
48	chr2:20648194-20648244	PFSK-1	brain:	n/a
49	chr2:20648194-20648244	T-47D	breast:	n/a
50	chr2:20648194-20648244	HAEpiC	amniotic membrane:	n/a

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20582061..20584787-chr2:20647277..20649666,2	MCF-7	breast:
2	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
3	chr2:20647037..20648776-chr6:43826398..43828925,2	MCF-7	breast:
4	chr2:20550911..20553369-chr2:20646204..20648737,2	K562	blood:
5	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
6	chr2:20647196..20649386-chr2:20825674..20827981,2	K562	blood:
7	chr2:20646857..20649701-chr2:20702827..20704331,2	K562	blood:
8	chr2:20647398..20650409-chr2:20654175..20656821,4	K562	blood:
9	chr2:20647262..20649198-chr3:105085481..105087426,2	MCF-7	breast:
10	chr2:20645830..20649178-chr2:20802657..20807893,7	MCF-7	breast:
11	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
12	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
13	chr2:20647610..20648406-chr8:146017221..146018201,2	Hela-S3	cervix:
14	chr2:20598069..20599864-chr2:20647082..20649646,2	MCF-7	breast:
15	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
16	chr2:20647607..20649619-chr4:103748419..103749985,2	MCF-7	breast:
17	chr17:57914924..57917331-chr2:20646962..20649237,2	MCF-7	breast:
18	chr2:20647633..20649474-chr2:20706759..20709106,2	MCF-7	breast:
19	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
20	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:
21	chr2:20647080..20649987-chr2:27272850..27275008,2	MCF-7	breast:
22	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
23	chr2:20611093..20611684-chr2:20647842..20648645,2	MCF-7	breast:
24	chr2:20646900..20649686-chr2:20739028..20740892,2	MCF-7	breast:
25	chr2:20647900..20649947-chr2:20748002..20750388,3	MCF-7	breast:
26	chr16:68268541..68270954-chr2:20645662..20648627,2	MCF-7	breast:
27	chr2:8821242..8823480-chr2:20647552..20650236,2	MCF-7	breast:
28	chr2:20593621..20596225-chr2:20647006..20648525,2	K562	blood:
29	chr2:20647678..20650094-chr2:20830839..20832383,2	K562	blood:
30	chr2:20645423..20650748-chr2:20698837..20705480,9	MCF-7	breast:
31	chr2:20646880..20648983-chr20:46681060..46683939,2	MCF-7	breast:
32	chr2:20647548..20649873-chr2:20806616..20809120,2	MCF-7	breast:
33	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
34	chr2:20574805..20576897-chr2:20646871..20649398,2	MCF-7	breast:
35	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	TF binding region
ENSG00000228950	CpG island
ENSG00000062716	Chromatin interaction
ENSG00000161016	Chromatin interaction
ENSG00000252216	Chromatin interaction
ENSG00000103067	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000084693	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000170017	Chromatin interaction
ENSG00000115738	Chromatin interaction
ENSG00000212171	Chromatin interaction
ENSG00000233416	Chromatin interaction
ENSG00000231636	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000235092	Chromatin interaction
ENSG00000227047	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1002162	0.87[CHD][hapmap]
rs11901246	0.81[CHD][hapmap]
rs13021908	0.81[CHD][hapmap]
rs13024532	0.92[ASN][1000 genomes]
rs1453051	0.87[CHD][hapmap]
rs342107	0.87[CHD][hapmap]
rs342114	0.87[CHD][hapmap]
rs342116	0.87[CHD][hapmap]
rs4666396	0.81[CHD][hapmap]
rs6531240	0.87[CHD][hapmap]
rs6715667	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers 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 target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv482049	chr2:20646835-20649200	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1062292	AC023137.2	cis	Artery Tibial	GTEx
rs1062292	PFN4	cis	parietal	SCAN
rs1062292	HS1BP3	cis	parietal	SCAN
rs1062292	FAM49A	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20643600-20650000	Active TSS	Right Atrium	heart
2	chr2:20644600-20650000	Active TSS	Psoas Muscle	Psoas
3	chr2:20645000-20650600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr2:20645400-20648600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:20645600-20648400	Active TSS	Brain Anterior Caudate	brain
6	chr2:20645600-20650000	Active TSS	Brain Angular Gyrus	brain
7	chr2:20646000-20648600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:20646000-20648600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:20646000-20648800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:20646000-20649000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:20646000-20649600	Active TSS	HSMMtube	muscle
12	chr2:20646000-20649800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:20646000-20650000	Active TSS	Ovary	ovary
14	chr2:20646000-20650200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:20646200-20648400	Active TSS	Fetal Lung	lung
16	chr2:20646200-20648600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:20646200-20648600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:20646200-20648600	Active TSS	HSMM	muscle
19	chr2:20646200-20649000	Active TSS	Fetal Kidney	kidney
20	chr2:20646200-20649000	Active TSS	Placenta Amnion	Placenta Amnion
21	chr2:20646200-20649000	Active TSS	Small Intestine	intestine
22	chr2:20646400-20648400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:20646400-20648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:20646400-20648400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:20646400-20648400	Active TSS	Placenta	Placenta
26	chr2:20646400-20648400	Active TSS	Hela-S3	cervix
27	chr2:20646400-20648400	Active TSS	Osteobl	bone
28	chr2:20646400-20648600	Active TSS	NH-A	brain
29	chr2:20646400-20649000	Bivalent/Poised TSS	HepG2	liver
30	chr2:20646400-20649200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:20646400-20649200	Active TSS	Fetal Intestine Large	intestine
32	chr2:20646400-20649400	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:20646400-20649400	Active TSS	Pancreas	Pancrea
34	chr2:20647000-20648600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr2:20647000-20648600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:20647000-20648600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
37	chr2:20647000-20648600	Transcr. at gene 5' and 3'	Right Ventricle	heart
38	chr2:20647000-20648600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
39	chr2:20647000-20648800	Flanking Active TSS	HMEC	breast
40	chr2:20647000-20649400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
41	chr2:20647200-20648600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr2:20647200-20648600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:20647200-20648600	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:20647200-20648600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr2:20647200-20648600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:20647200-20648600	Transcr. at gene 5' and 3'	NHLF	lung
47	chr2:20647200-20648800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:20647200-20649000	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
49	chr2:20647200-20649400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:20647200-20649400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links