Variant report

Variant	rs7975271
Chromosome Location	chr12:25252410-25252411
allele	C/T
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	chr12:25251979-25252612	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:25251550-25252448	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:25250809-25252650	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:25251662-25252602	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10505959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10771165	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10771166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10771174	0.89[CHB][hapmap]
rs10771175	1.00[CHB][hapmap]
rs10771176	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs10842463	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10842464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10842467	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842468	0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842470	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10842490	1.00[CHB][hapmap]
rs11047825	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047843	0.86[ASN][1000 genomes]
rs11047858	0.89[CHB][hapmap]
rs11047885	1.00[CHB][hapmap]
rs11834088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12227966	1.00[CHB][hapmap]
rs12228364	0.98[ASN][1000 genomes]
rs12228365	0.98[ASN][1000 genomes]
rs12228638	1.00[CHB][hapmap]
rs12367971	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1497253	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17386824	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2220196	1.00[CHB][hapmap]
rs3924650	1.00[CHB][hapmap]
rs4313666	1.00[CHB][hapmap]
rs57544299	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134616	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303373	1.00[CHB][hapmap]
rs7303669	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7960092	0.93[ASN][1000 genomes]
rs7960428	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960917	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7964195	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7971062	1.00[CHB][hapmap]
rs7971288	1.00[CHB][hapmap]
rs7972632	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973450	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7976145	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976355	0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7977670	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7980769	1.00[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7975271	SSPN	cis	parietal	SCAN
rs7975271	CRTAP	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
6	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
8	chr12:25238600-25265200	Weak transcription	Lung	lung
9	chr12:25239800-25253200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:25246400-25252600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:25246400-25264000	Weak transcription	Ovary	ovary
14	chr12:25247400-25253000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
16	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
17	chr12:25248000-25253000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:25248600-25252600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:25248600-25257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:25248800-25255800	Strong transcription	Thymus	Thymus
24	chr12:25248800-25258000	Strong transcription	Dnd41	blood
25	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:25250000-25253200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:25250600-25256000	Weak transcription	Esophagus	oesophagus
30	chr12:25251000-25254000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:25251000-25254200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:25251400-25253200	Genic enhancers	GM12878-XiMat	blood
33	chr12:25251400-25254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:25251400-25255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:25251800-25253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
37	chr12:25252000-25254000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:25252000-25254600	Weak transcription	Liver	Liver
39	chr12:25252000-25254800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:25252200-25254000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:25252200-25257000	Weak transcription	Fetal Intestine Large	intestine
42	chr12:25252200-25264000	Weak transcription	Spleen	Spleen
43	chr12:25252400-25260400	Weak transcription	Adipose Nuclei	Adipose

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