Variant report

Variant	rs7312857
Chromosome Location	chr12:51707626-51707627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10876156	0.80[CEU][hapmap]
rs11341	1.00[CEU][hapmap]
rs12578771	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580302	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580599	0.83[CHB][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap];0.80[ASN][1000 genomes]
rs12581282	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17860277	0.86[EUR][1000 genomes]
rs17860287	0.90[EUR][1000 genomes]
rs17860296	0.92[EUR][1000 genomes]
rs17860299	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs17860302	0.92[EUR][1000 genomes]
rs17860317	0.93[CEU][hapmap]
rs17860346	0.87[EUR][1000 genomes]
rs17860364	0.86[EUR][1000 genomes]
rs17860365	0.87[EUR][1000 genomes]
rs17860378	0.86[EUR][1000 genomes]
rs17860380	0.87[EUR][1000 genomes]
rs17860382	0.87[EUR][1000 genomes]
rs17860387	0.87[EUR][1000 genomes]
rs2288367	0.93[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3782470	0.93[CEU][hapmap]
rs3858637	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3969069	0.82[CEU][hapmap]
rs4335588	0.83[ASN][1000 genomes]
rs4761881	0.93[CEU][hapmap]
rs55901988	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56869579	0.85[ASN][1000 genomes]
rs57484374	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58213562	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58673573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60641385	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60797544	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61172662	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61380773	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61570206	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61605107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580821	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs7133314	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7135736	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs7138394	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7301933	0.86[ASN][1000 genomes]
rs7308177	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7311196	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7316221	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7316301	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316604	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74093810	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74093814	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74093823	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74093827	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74093853	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954976	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs7975715	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7312857	FAM186B	cis	parietal	SCAN
rs7312857	ZNF641	cis	cerebellum	SCAN
rs7312857	COL2A1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51681800-51714200	Weak transcription	Gastric	stomach
2	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
3	chr12:51696600-51712400	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr12:51698400-51712600	Weak transcription	Spleen	Spleen
5	chr12:51699200-51709400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
6	chr12:51699800-51710000	Strong transcription	Fetal Thymus	thymus
7	chr12:51700600-51711000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:51701400-51708600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:51701600-51708400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:51702200-51712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:51702400-51709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:51702400-51712200	Weak transcription	GM12878-XiMat	blood
13	chr12:51702600-51709000	Weak transcription	K562	blood
14	chr12:51702800-51712200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:51703200-51709800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:51703400-51711200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr12:51703400-51711200	Weak transcription	Placenta	Placenta
18	chr12:51704000-51712200	Weak transcription	Stomach Mucosa	stomach
19	chr12:51704400-51712200	Weak transcription	A549	lung
20	chr12:51704600-51712600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:51705600-51707800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:51705600-51708200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:51706000-51707800	Strong transcription	Primary B cells from cord blood	blood
24	chr12:51706400-51707800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:51706400-51708200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:51706600-51709400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:51706800-51709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:51707200-51708400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:51707400-51707800	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:51707400-51708800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:51707400-51712400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:51707600-51708600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:51707600-51708800	Enhancers	Primary T cells from cord blood	blood
34	chr12:51707600-51709400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:51707600-51709600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:51707600-51712600	Weak transcription	Duodenum Mucosa	Duodenum

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