Variant report

Variant	rs12088810
Chromosome Location	chr1:46153290-46153291
allele	C/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	POLR2A	chr1:46151822-46154262	Hela-S3	cervix:	n/a	n/a
2	EP300	chr1:46151468-46153308	ECC-1	luminal epithelium:	n/a	n/a
3	CBX3	chr1:46151923-46154488	K562	blood:	n/a	n/a
4	TAF1	chr1:46152803-46153359	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:46151616-46154521	K562	blood:	n/a	n/a
6	POLR2A	chr1:46153267-46154554	PANC-1	pancreas:	n/a	n/a
7	NRF1	chr1:46152090-46153382	GM12878	blood:	n/a	chr1:46152409-46152418 chr1:46152316-46152327
8	RELA	chr1:46151691-46154515	GM19193	blood:	n/a	n/a
9	MYC	chr1:46151662-46154635	NB4	blood:	n/a	chr1:46153143-46153152 chr1:46154273-46154282 chr1:46154271-46154281 chr1:46154272-46154283 chr1:46154272-46154283
10	POLR2A	chr1:46151872-46154297	HUVEC	blood vessel:	n/a	n/a
11	RELA	chr1:46151475-46154604	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:46151668-46154235	GM12878	blood:	n/a	n/a
13	RELA	chr1:46152079-46154531	GM19099	blood:	n/a	n/a
14	POLR2A	chr1:46151735-46153349	IMR90	lung:	n/a	n/a
15	POLR2A	chr1:46151715-46154301	GM12878	blood:	n/a	n/a
16	NFATC1	chr1:46151371-46153339	GM12878	blood:	n/a	n/a
17	POU2F2	chr1:46151875-46153659	GM12891	blood:	n/a	chr1:46152412-46152424 chr1:46151883-46151895
18	TAF1	chr1:46151655-46154407	GM12878	blood:	n/a	n/a
19	KAP1	chr1:46151137-46154372	U2OS	brain:	n/a	chr1:46152984-46152992
20	ETS1	chr1:46151613-46153300	K562	blood:	n/a	chr1:46152830-46152843 chr1:46153218-46153232 chr1:46153220-46153231 chr1:46152831-46152844 chr1:46152409-46152420 chr1:46151887-46151898
21	POLR2A	chr1:46151635-46154478	PFSK-1	brain:	n/a	n/a
22	IRF1	chr1:46151097-46154537	K562	blood:	n/a	chr1:46152405-46152419 chr1:46151132-46151144 chr1:46153367-46153377 chr1:46153067-46153084 chr1:46151681-46151695
23	TEAD4	chr1:46151021-46154533	K562	blood:	n/a	n/a
24	POLR2A	chr1:46151710-46153292	HUVEC	blood vessel:	n/a	n/a
25	TBL1XR1	chr1:46151650-46154451	GM12878	blood:	n/a	n/a
26	MAZ	chr1:46151361-46154357	GM12878	blood:	n/a	chr1:46153143-46153152 chr1:46154273-46154282 chr1:46154272-46154283 chr1:46154272-46154283
27	POLR2A	chr1:46151595-46154375	HCT-116	colon:	n/a	n/a
28	ELF1	chr1:46152021-46153307	MCF-7	breast:	n/a	n/a
29	POLR2A	chr1:46151616-46154527	U87	brain:	n/a	n/a
30	RCOR1	chr1:46151696-46153369	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:46151861-46153421	ProgFib	skin:	n/a	n/a
32	NFIC	chr1:46151360-46153304	ECC-1	luminal epithelium:	n/a	chr1:46151772-46151788
33	POLR2A	chr1:46151782-46153339	MCF-7	breast:	n/a	n/a
34	YY1	chr1:46152778-46153296	HepG2	liver:	n/a	n/a
35	IRF1	chr1:46151310-46154420	K562	blood:	n/a	chr1:46152405-46152419 chr1:46153367-46153377 chr1:46153067-46153084 chr1:46151681-46151695
36	SMC3	chr1:46152842-46153363	HepG2	liver:	n/a	n/a
37	TBL1XR1	chr1:46151001-46154461	K562	blood:	n/a	n/a
38	ETS1	chr1:46152102-46153318	A549	lung:	n/a	chr1:46152830-46152843 chr1:46153218-46153232 chr1:46153220-46153231 chr1:46152831-46152844 chr1:46152409-46152420
39	RCOR1	chr1:46151993-46154382	K562	blood:	n/a	n/a
40	POLR2A	chr1:46151926-46153335	Hela-S3	cervix:	n/a	n/a
41	USF2	chr1:46152476-46154020	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:46151780-46154266	K562	blood:	n/a	n/a
43	ARID3A	chr1:46151681-46154258	HepG2	liver:	n/a	n/a
44	MXI1	chr1:46151207-46154495	GM12878	blood:	n/a	n/a
45	UBTF	chr1:46151620-46154026	K562	blood:	n/a	n/a
46	STAT3	chr1:46152586-46154453	GM12878	blood:	n/a	chr1:46152862-46152874
47	CREB1	chr1:46151691-46153443	GM12878	blood:	n/a	n/a
48	RELA	chr1:46151854-46154474	GM15510	blood:	n/a	n/a
49	POLR2A	chr1:46151798-46154204	GM12878	blood:	n/a	n/a
50	HCFC1	chr1:46151681-46154389	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46150825..46154977-chr1:46267620..46271634,6	MCF-7	breast:
2	chr1:46152208..46153875-chr12:104323647..104326577,2	K562	blood:
3	chr1:45986006..45987608-chr1:46151069..46153462,2	MCF-7	breast:
4	chr1:46149445..46155578-chr1:46213291..46217457,7	MCF-7	breast:
5	chr1:46150526..46156032-chr1:46265067..46272923,24	K562	blood:
6	chr1:46152780..46153573-chr11:62358582..62359536,2	NB4	blood:
7	chr1:46150273..46155270-chr1:46767408..46770700,6	K562	blood:
8	chr1:46151204..46153647-chr1:46767504..46769158,2	K562	blood:
9	chr1:46152318..46155647-chr1:46160597..46165176,4	MCF-7	breast:
10	chr1:46150194..46156123-chr1:46211510..46222859,25	K562	blood:
11	chr1:45985920..45989261-chr1:46150872..46154561,4	K562	blood:
12	chr1:46048069..46054740-chr1:46150080..46155979,19	K562	blood:
13	chr1:46152732..46153451-chr14:90420503..90421025,2	Hela-S3	cervix:
14	chr1:46123716..46126422-chr1:46150615..46153415,2	MCF-7	breast:
15	chr1:46152739..46153727-chr12:1100153..1101024,2	NB4	blood:
16	chr1:46151257..46156483-chr1:46213184..46217414,6	MCF-7	breast:
17	chr1:45195169..45196980-chr1:46153286..46155676,3	K562	blood:
18	chr1:46113919..46122142-chr1:46149927..46154523,9	K562	blood:
19	chr1:46151352..46155002-chr1:46160340..46164290,4	MCF-7	breast:
20	chr1:46152742..46154497-chr1:46598104..46600234,2	K562	blood:
21	chr1:46153059..46154039-chr1:46216203..46216739,2	MCF-7	breast:
22	chr1:45185676..45189343-chr1:46151396..46155571,4	K562	blood:
23	chr1:46048446..46052403-chr1:46150752..46155740,15	K562	blood:
24	chr1:46149977..46154848-chr1:46211592..46220262,26	K562	blood:
25	chr1:45804320..45807297-chr1:46151085..46154859,4	K562	blood:
26	chr1:46151101..46153559-chr2:242663835..242666303,2	K562	blood:
27	chr1:45284131..45287086-chr1:46150918..46155233,4	K562	blood:
28	chr1:46101052..46102818-chr1:46152113..46153936,2	K562	blood:
29	chr1:46152331..46153862-chr1:46251195..46252754,2	K562	blood:
30	chr1:46153160..46153905-chr16:278939..279745,2	Hela-S3	cervix:
31	chr1:46152798..46153298-chr18:3012485..3013343,2	Hela-S3	cervix:
32	chr1:45984465..45989261-chr1:46150683..46156386,7	K562	blood:
33	chr1:46151080..46154672-chr1:46265067..46271759,20	K562	blood:
34	chr1:46149604..46155141-chr1:46267151..46271003,9	MCF-7	breast:

Variant related genes	Relation type
TMEM69	TF binding region
GPBP1L1	TF binding region
ENSG00000168395	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000227857	Chromatin interaction
ENSG00000007392	Chromatin interaction
ENSG00000259053	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000250132	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000101577	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000086015	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000235351	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000140025	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000230896	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000234329	Chromatin interaction
ENSG00000149016	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11211127	1.00[AMR][1000 genomes]
rs11211144	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211148	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211150	1.00[YRI][hapmap]
rs11211153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211154	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211155	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12057167	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12063380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12067882	1.00[AMR][1000 genomes]
rs12070146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	1.00[AMR][1000 genomes]
rs12077112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081121	1.00[AMR][1000 genomes]
rs12082672	1.00[AMR][1000 genomes]
rs12085372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086880	1.00[AMR][1000 genomes]
rs12091335	1.00[AMR][1000 genomes]
rs12091360	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093444	1.00[AMR][1000 genomes]
rs12094011	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs16832550	1.00[AMR][1000 genomes]
rs16832553	1.00[AMR][1000 genomes]
rs16832557	1.00[AMR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	1.00[AMR][1000 genomes]
rs28548585	1.00[AMR][1000 genomes]
rs28576912	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28607905	1.00[AMR][1000 genomes]
rs35067820	1.00[AMR][1000 genomes]
rs35808563	1.00[AMR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs668289	1.00[AMR][1000 genomes]
rs6690210	1.00[YRI][hapmap]
rs669417	1.00[AMR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs7550744	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46148800-46155000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:46149600-46154200	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:46149600-46154800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:46149600-46155600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:46149800-46155000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:46150000-46154400	Active TSS	Thymus	Thymus
7	chr1:46150000-46154800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:46150000-46154800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:46150000-46154800	Active TSS	Psoas Muscle	Psoas
10	chr1:46150000-46154800	Active TSS	GM12878-XiMat	blood
11	chr1:46150200-46153400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:46150200-46154400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:46150200-46154600	Active TSS	Aorta	Aorta
14	chr1:46150200-46154600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:46150200-46155000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:46150200-46155000	Active TSS	Right Ventricle	heart
17	chr1:46150200-46155200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:46150400-46153400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:46150400-46154200	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:46150400-46154400	Active TSS	Brain Hippocampus Middle	brain
21	chr1:46150400-46154600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:46150400-46154600	Active TSS	Colon Smooth Muscle	Colon
23	chr1:46150400-46154800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:46150400-46154800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:46150400-46155000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:46150400-46155000	Active TSS	K562	blood
27	chr1:46150600-46153400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:46150600-46154800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:46150600-46154800	Active TSS	Colonic Mucosa	Colon
30	chr1:46150800-46154400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:46150800-46155200	Active TSS	A549	lung
32	chr1:46151000-46153400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:46151000-46154400	Active TSS	Brain Angular Gyrus	brain
34	chr1:46151000-46154400	Active TSS	Brain Anterior Caudate	brain
35	chr1:46151000-46154400	Active TSS	Brain Cingulate Gyrus	brain
36	chr1:46151000-46154400	Active TSS	Brain Substantia Nigra	brain
37	chr1:46151000-46154400	Active TSS	Fetal Muscle Trunk	muscle
38	chr1:46151000-46154400	Active TSS	Left Ventricle	heart
39	chr1:46151000-46154600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:46151000-46154600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:46151000-46154600	Active TSS	Esophagus	oesophagus
42	chr1:46151000-46154600	Active TSS	Lung	lung
43	chr1:46151000-46154600	Active TSS	Ovary	ovary
44	chr1:46151000-46154600	Active TSS	Pancreas	Pancrea
45	chr1:46151000-46154600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr1:46151000-46154600	Active TSS	Small Intestine	intestine
47	chr1:46151000-46154800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:46151000-46154800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:46151000-46154800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:46151000-46155000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links