Variant report

Variant	rs7960917
Chromosome Location	chr12:25361646-25361647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:25360345..25363187-chr12:25402530..25405370,3	MCF-7	breast:
2	chr12:25351123..25353485-chr12:25360688..25362521,2	K562	blood:
3	chr12:25350292..25353485-chr12:25360688..25363918,3	K562	blood:
4	chr12:25361412..25364076-chr12:25538514..25540823,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133703	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10505959	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs10743548	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771166	1.00[CHB][hapmap]
rs10771174	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10771175	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs10771176	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs10771183	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842464	1.00[CHB][hapmap]
rs10842468	0.88[JPT][hapmap]
rs10842470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10842490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10842503	0.88[ASN][1000 genomes]
rs10842515	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10842516	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10842517	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11047825	0.88[CHB][hapmap]
rs11047858	0.89[CHB][hapmap]
rs11047878	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047879	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047904	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047908	0.90[ASN][1000 genomes]
rs11047912	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11047914	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11047917	1.00[JPT][hapmap]
rs1137282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834088	1.00[CHB][hapmap]
rs11836509	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227966	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12228638	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs12367971	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs1497253	0.89[CHB][hapmap]
rs17388573	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17388587	1.00[JPT][hapmap]
rs17389103	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2220196	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3924650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4313666	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4368021	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs4606562	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61761150	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61762422	0.81[ASN][1000 genomes]
rs7133640	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7134616	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs7137734	1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7298444	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7299998	0.84[MKK][hapmap]
rs7303373	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs7303669	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7309670	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7315339	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7960428	1.00[CHB][hapmap]
rs7964623	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965763	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7968023	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7971062	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7971288	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7973450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973623	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975271	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7976254	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs7976355	1.00[JPT][hapmap]
rs7977616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980834	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7960917	SSPN	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
5	chr12:25349000-25374200	Weak transcription	Lung	lung
6	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
7	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
8	chr12:25349200-25362400	Weak transcription	Colonic Mucosa	Colon
9	chr12:25349200-25363200	Weak transcription	Brain Substantia Nigra	brain
10	chr12:25349200-25363400	Weak transcription	Stomach Mucosa	stomach
11	chr12:25349400-25367400	Weak transcription	Fetal Stomach	stomach
12	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:25349400-25388600	Weak transcription	NHLF	lung
14	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
17	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
18	chr12:25349600-25364600	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
26	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
27	chr12:25349800-25390200	Weak transcription	K562	blood
28	chr12:25350000-25372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:25350000-25402800	Weak transcription	Ovary	ovary
30	chr12:25353200-25378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:25354400-25368200	Weak transcription	HUVEC	blood vessel
33	chr12:25354400-25369000	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:25354400-25378400	Weak transcription	HMEC	breast
35	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
36	chr12:25354600-25389000	Weak transcription	HSMMtube	muscle
37	chr12:25355200-25362600	Strong transcription	Fetal Thymus	thymus
38	chr12:25355400-25366000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:25355400-25370600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:25355600-25363400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:25355800-25362000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:25355800-25363400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:25355800-25363400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:25355800-25366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
46	chr12:25356000-25362200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:25356000-25363400	Strong transcription	Dnd41	blood
48	chr12:25356000-25363600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:25356000-25363800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:25356200-25363200	Strong transcription	Primary B cells from cord blood	blood

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