Variant report

Variant	rs7976254
Chromosome Location	chr12:25256354-25256355
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	chr12:25253071-25257079	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000258449	TF binding region
LRMP	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10505959	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505980	0.82[JPT][hapmap]
rs10771165	0.87[ASN][1000 genomes]
rs10771166	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10771169	0.83[ASN][1000 genomes]
rs10771174	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs10771175	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10771176	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs10842463	0.87[ASN][1000 genomes]
rs10842464	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10842467	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842468	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842469	0.88[ASN][1000 genomes]
rs10842470	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10842471	0.88[ASN][1000 genomes]
rs10842472	0.81[ASN][1000 genomes]
rs10842490	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10842514	0.82[JPT][hapmap]
rs10842515	0.90[JPT][hapmap]
rs10842516	0.90[JPT][hapmap]
rs10842517	0.90[JPT][hapmap]
rs11047825	0.84[CEU][hapmap];0.88[CHB][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047843	0.96[ASN][1000 genomes]
rs11047858	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11047885	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11047912	0.90[JPT][hapmap]
rs11047914	0.90[JPT][hapmap]
rs11047915	0.82[JPT][hapmap]
rs11047917	0.90[JPT][hapmap]
rs11047919	0.82[JPT][hapmap]
rs11834088	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12226937	0.82[JPT][hapmap]
rs12227966	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12228364	0.87[ASN][1000 genomes]
rs12228365	0.87[ASN][1000 genomes]
rs12228638	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs12367971	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs12425900	0.89[JPT][hapmap]
rs12813551	0.82[JPT][hapmap]
rs1497253	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs17386824	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17388587	0.90[JPT][hapmap]
rs17389103	0.90[JPT][hapmap]
rs2220196	1.00[CHB][hapmap]
rs2883030	0.81[ASN][1000 genomes]
rs3924650	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4313666	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4368021	0.90[JPT][hapmap]
rs4963859	0.90[JPT][hapmap]
rs57544299	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487458	0.81[ASN][1000 genomes]
rs6487464	0.82[JPT][hapmap]
rs7133640	0.90[JPT][hapmap]
rs7133904	0.83[ASN][1000 genomes]
rs7134616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135130	0.81[ASN][1000 genomes]
rs7303373	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7303669	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs7303889	0.83[YRI][hapmap]
rs7309670	0.89[JPT][hapmap]
rs7315339	0.90[JPT][hapmap]
rs7956818	0.81[ASN][1000 genomes]
rs7960092	0.82[ASN][1000 genomes]
rs7960428	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7960917	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7964195	0.87[ASN][1000 genomes]
rs7971062	1.00[CHB][hapmap]
rs7971288	1.00[CHB][hapmap]
rs7972632	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973365	0.81[ASN][1000 genomes]
rs7973450	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7975271	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]
rs7976145	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976355	1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977670	0.87[ASN][1000 genomes]
rs7980769	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][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
rs7976254	SSPN	cis	parietal	SCAN
rs7976254	CRTAP	trans	parietal	SCAN

Chromatin state (count:42 , 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	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
5	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
7	chr12:25238600-25265200	Weak transcription	Lung	lung
8	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:25246400-25264000	Weak transcription	Ovary	ovary
11	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
12	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
13	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:25248600-25257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:25248800-25258000	Strong transcription	Dnd41	blood
18	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
22	chr12:25252200-25257000	Weak transcription	Fetal Intestine Large	intestine
23	chr12:25252200-25264000	Weak transcription	Spleen	Spleen
24	chr12:25252400-25260400	Weak transcription	Adipose Nuclei	Adipose
25	chr12:25253200-25262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:25254000-25257000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:25254000-25257400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:25254000-25260200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:25254200-25259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:25254200-25260400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:25254200-25263600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:25254200-25263800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:25254200-25263800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:25254400-25260600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:25254800-25257400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr12:25254800-25257600	Strong transcription	GM12878-XiMat	blood
37	chr12:25255600-25260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:25255800-25260200	Weak transcription	Thymus	Thymus
39	chr12:25255800-25261400	Weak transcription	Small Intestine	intestine
40	chr12:25255800-25262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:25256000-25260400	Weak transcription	Liver	Liver
42	chr12:25256000-25265200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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