Variant report

Variant	rs895951
Chromosome Location	chr12:122237115-122237116
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	chr12:122236930-122238478	A549	lung:	n/a	chr12:122237618-122237634 chr12:122238028-122238044 chr12:122238027-122238043
2	NR2F2	chr12:122237005-122238266	K562	blood:	n/a	n/a
3	POLR2A	chr12:122234779-122241623	PANC-1	pancreas:	n/a	n/a
4	TEAD4	chr12:122236947-122237624	K562	blood:	n/a	n/a
5	POLR2A	chr12:122234914-122237514	HepG2	liver:	n/a	n/a
6	WRNIP1	chr12:122237105-122237136	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:122234803-122242201	K562	blood:	n/a	n/a
8	HEY1	chr12:122234874-122237595	K562	blood:	n/a	n/a
9	CEBPB	chr12:122236960-122237262	ECC-1	luminal epithelium:	n/a	chr12:122237089-122237100
10	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
11	HEY1	chr12:122237033-122237622	HepG2	liver:	n/a	n/a
12	MXI1	chr12:122234637-122245085	SK-N-SH	brain:	n/a	n/a
13	CEBPB	chr12:122236922-122237605	K562	blood:	n/a	chr12:122237089-122237100
14	TBP	chr12:122237079-122242074	K562	blood:	n/a	chr12:122237265-122237276
15	POLR2A	chr12:122236670-122237181	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:122234794-122240414	K562	blood:	n/a	n/a
17	KAP1	chr12:122235976-122237502	HEK293	kidney:	n/a	n/a
18	POLR2A	chr12:122235732-122237166	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOS	chr12:122237055-122237181	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:122236872-122242965	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:122236861-122241446	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:122237002-122240263	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr12:122237004-122237269	H1-hESC	embryonic stem cell:	n/a	chr12:122237089-122237100
24	POLR2A	chr12:122231231-122242190	PANC-1	pancreas:	n/a	n/a
25	JUN	chr12:122235808-122238372	K562	blood:	n/a	chr12:122237627-122237636 chr12:122237624-122237633 chr12:122237625-122237634 chr12:122238064-122238073 chr12:122238349-122238358 chr12:122237626-122237635 chr12:122238274-122238283
26	HDAC2	chr12:122237084-122237597	K562	blood:	n/a	chr12:122237307-122237321
27	POLR2A	chr12:122234878-122240352	K562	blood:	n/a	n/a
28	REST	chr12:122236716-122237588	A549	lung:	n/a	n/a
29	REST	chr12:122236903-122243598	H1-neurons	neurons:	n/a	chr12:122238975-122238995 chr12:122239330-122239343 chr12:122238885-122238898 chr12:122238953-122238966 chr12:122242500-122242508 chr12:122238960-122238969 chr12:122239946-122239956
30	POLR2A	chr12:122236702-122237606	GM12891	blood:	n/a	n/a
31	EP300	chr12:122236939-122237404	HepG2	liver:	n/a	n/a
32	CEBPB	chr12:122236942-122237303	A549	lung:	n/a	chr12:122237089-122237100
33	POLR2A	chr12:122237041-122237600	HUVEC	blood vessel:	n/a	n/a
34	CEBPB	chr12:122237026-122237236	HepG2	liver:	n/a	chr12:122237089-122237100
35	POLR2A	chr12:122229221-122241674	GM12892	blood:	n/a	n/a
36	CEBPB	chr12:122236943-122237497	IMR90	lung:	n/a	chr12:122237089-122237100
37	EP300	chr12:122236983-122238390	A549	lung:	n/a	chr12:122237618-122237634 chr12:122238028-122238044 chr12:122238027-122238043
38	POLR2A	chr12:122234846-122241668	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr12:122236825-122237614	U87	brain:	n/a	n/a
40	TCF12	chr12:122234834-122241830	A549	lung:	n/a	chr12:122236861-122236868 chr12:122241766-122241776 chr12:122239945-122239955 chr12:122235313-122235323 chr12:122235971-122235978 chr12:122237372-122237382
41	HEY1	chr12:122236932-122237197	HepG2	liver:	n/a	n/a
42	MXI1	chr12:122234897-122240491	IMR90	lung:	n/a	n/a
43	TEAD4	chr12:122236087-122238284	K562	blood:	n/a	n/a
44	ZNF263	chr12:122234968-122240263	HEK293-T-REx	kidney:	n/a	chr12:122235729-122235738 chr12:122236392-122236401 chr12:122234969-122234978 chr12:122238933-122238942
45	POLR2A	chr12:122234862-122237596	GM12878	blood:	n/a	n/a
46	MYC	chr12:122235896-122239171	K562	blood:	n/a	chr12:122236273-122236286 chr12:122236274-122236284 chr12:122238516-122238525 chr12:122237622-122237632 chr12:122236274-122236285 chr12:122236274-122236285
47	POLR2A	chr12:122237052-122237621	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr12:122236688-122237134	Hela-S3	cervix:	n/a	n/a
49	EGR1	chr12:122236889-122238561	HCT-116	colon:	n/a	chr12:122238536-122238549 chr12:122238456-122238465 chr12:122237627-122237640 chr12:122237367-122237381 chr12:122237625-122237635 chr12:122237369-122237378 chr12:122237624-122237634 chr12:122237972-122237986 chr12:122237626-122237636 chr12:122238145-122238155 chr12:122237996-122238010
50	CEBPB	chr12:122236942-122237299	HepG2	liver:	n/a	chr12:122237089-122237100

No.	Distal block	Cell Line	Cell type
1	chr12:121994481..121996549-chr12:122235524..122237338,2	MCF-7	breast:
2	chr12:122235984..122238947-chr2:74211072..74214040,3	MCF-7	breast:
3	chr12:122207619..122210268-chr12:122236043..122238040,2	K562	blood:
4	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
5	chr12:122236965..122238991-chr12:122683290..122686252,2	K562	blood:
6	chr11:45928634..45930948-chr12:122237013..122238884,2	MCF-7	breast:
7	chr12:122237036..122238620-chr12:122459729..122461311,2	K562	blood:
8	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
9	chr12:122237028..122239073-chr12:122370482..122372481,2	K562	blood:
10	chr12:122235746..122237932-chr12:122463152..122466660,3	K562	blood:
11	chr12:122235892..122238477-chr2:235091344..235092959,2	MCF-7	breast:
12	chr12:122235556..122237651-chr14:35867580..35869570,2	MCF-7	breast:
13	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
14	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
15	chr12:120727962..120730106-chr12:122235107..122237468,3	K562	blood:
16	chr12:122237008..122237974-chr12:122249958..122250519,2	MCF-7	breast:
17	chr12:122235189..122237423-chr17:56708263..56710518,2	MCF-7	breast:
18	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
19	chr12:122193178..122194758-chr12:122236438..122238242,2	K562	blood:
20	chr12:122236992..122238955-chr17:57923665..57925298,2	MCF-7	breast:
21	chr12:122235040..122237798-chr4:15655451..15658367,2	MCF-7	breast:
22	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
23	chr12:122236856..122239163-chr12:122456320..122458969,2	K562	blood:
24	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOF-1	chr12:122237078-122237563	ENSG00000212694.4
2	lnc-RHOF-1	chr12:122234097-122237538	NONHSAT031449
3	lnc-RHOF-1	chr12:122235738-122239714	NONHSAT031462

Variant related genes	Relation type
ENSG00000212694	TF binding region
SETD1B	TF binding region
RHOF	TF binding region
ENSG00000201524	Chromatin interaction
ENSG00000158113	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000234776	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000255856	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004390	0.91[EUR][1000 genomes]
rs11043202	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043207	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1168663	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168664	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168665	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168666	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs1168668	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168669	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168671	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168673	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12307227	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313997	0.89[ASN][1000 genomes]
rs12314801	0.89[ASN][1000 genomes]
rs12820413	0.82[ASN][1000 genomes]
rs12823194	0.85[EUR][1000 genomes]
rs1667578	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1667579	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1795965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795966	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2019561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019562	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2122266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2707057	0.82[ASN][1000 genomes]
rs2707066	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2707067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712852	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957564	0.91[EUR][1000 genomes]
rs7974348	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs895952	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs895957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921286	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930665	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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 target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs895951	LOC338799	cis	parietal	SCAN
rs895951	CCDC60	cis	parietal	SCAN
rs895951	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx
rs895951	SBNO1	cis	parietal	SCAN
rs895951	LOC338799	cis	cerebellum	SCAN
rs895951	MPHOSPH9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122232800-122238000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:122233000-122237200	Genic enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:122233000-122237200	Genic enhancers	Fetal Lung	lung
4	chr12:122233200-122237200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:122234000-122237600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:122234200-122237600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr12:122234400-122237200	Transcr. at gene 5' and 3'	K562	blood
8	chr12:122234400-122237600	Flanking Active TSS	HSMM	muscle
9	chr12:122234400-122238000	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr12:122234800-122237400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:122234800-122237400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
12	chr12:122235000-122237200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:122235000-122237200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
14	chr12:122235000-122237400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:122235000-122237400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:122235000-122237400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:122235000-122237400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr12:122235000-122237400	Flanking Active TSS	Pancreas	Pancrea
19	chr12:122235000-122237400	Flanking Active TSS	Osteobl	bone
20	chr12:122235000-122237600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:122235000-122237600	Flanking Active TSS	NH-A	brain
22	chr12:122235000-122237600	Flanking Active TSS	NHEK	skin
23	chr12:122235000-122238000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:122235000-122238000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
25	chr12:122235200-122237200	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
26	chr12:122235200-122237400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr12:122235200-122245400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:122235400-122237200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
29	chr12:122235400-122237200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:122235400-122237400	Flanking Active TSS	Liver	Liver
31	chr12:122235400-122237400	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr12:122235400-122237400	Flanking Active TSS	HepG2	liver
33	chr12:122235400-122237800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:122235400-122239800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
35	chr12:122235600-122237200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:122235600-122237200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
37	chr12:122235600-122237200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:122235600-122237400	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr12:122235600-122238200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:122235800-122237200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
41	chr12:122235800-122237200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:122235800-122237200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:122235800-122237200	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr12:122235800-122237200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
45	chr12:122235800-122237400	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr12:122235800-122237400	Transcr. at gene 5' and 3'	Thymus	Thymus
47	chr12:122235800-122239400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
48	chr12:122236000-122237200	Genic enhancers	H9 Cell Line	embryonic stem cell
49	chr12:122236000-122237200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr12:122236000-122237200	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood

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