Variant report

Variant	rs6487464
Chromosome Location	chr12:25391456-25391457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:25391008..25395226-chr12:25537516..25540664,6	MCF-7	breast:
2	chr12:25382080..25386117-chr12:25388802..25392255,4	MCF-7	breast:
3	chr12:25390084..25393498-chr12:25395156..25398677,4	K562	blood:
4	chr12:25390084..25392027-chr12:25396306..25398130,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10505959	0.82[JPT][hapmap]
rs10505960	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs10505980	0.94[ASW][hapmap];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];0.97[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842492	0.91[JPT][hapmap]
rs10842494	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs10842496	0.83[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap]
rs10842498	0.84[JPT][hapmap]
rs10842501	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10842502	0.84[JPT][hapmap]
rs10842504	0.92[JPT][hapmap]
rs10842505	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10842514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10842518	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047865	0.84[JPT][hapmap]
rs11047887	0.92[JPT][hapmap]
rs11047888	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs11047894	1.00[JPT][hapmap]
rs11047901	0.92[JPT][hapmap]
rs11047902	0.92[JPT][hapmap]
rs11047915	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047919	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs1137188	0.92[JPT][hapmap]
rs12226937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368504	0.80[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs12423443	0.84[JPT][hapmap]
rs12579073	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs12579942	0.80[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs12587	0.80[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs12810577	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs12813551	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815546	0.80[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs12822857	0.92[JPT][hapmap]
rs13096	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs17329025	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs2291365	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs2352782	0.84[JPT][hapmap]
rs34527025	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4246229	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs4309240	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397950	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531569	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4559767	0.84[JPT][hapmap]
rs4963859	1.00[JPT][hapmap]
rs4963860	0.92[JPT][hapmap]
rs712	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7297103	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs7298636	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7299998	1.00[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap]
rs7302922	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7306769	0.83[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap]
rs7308865	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs7976254	0.82[JPT][hapmap]
rs9266	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs9634100	0.83[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv470279	chr12:25384658-25399121	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv898927	chr12:25389220-25408047	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6487464	SSPN	cis	parietal	SCAN

Chromatin state (count:119 , 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	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
4	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
7	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
8	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:25350000-25402800	Weak transcription	Ovary	ovary
14	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
16	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
17	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
18	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:25361000-25395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
22	chr12:25362000-25402400	Weak transcription	HepG2	liver
23	chr12:25365200-25393800	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:25372400-25402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:25373000-25393800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:25374400-25391600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:25374800-25402600	Weak transcription	Placenta	Placenta
28	chr12:25375000-25402800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:25377800-25402200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:25377800-25402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:25378800-25401800	Weak transcription	Adipose Nuclei	Adipose
32	chr12:25380400-25402200	Weak transcription	Fetal Lung	lung
33	chr12:25380600-25393800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:25381000-25395400	Weak transcription	HUVEC	blood vessel
35	chr12:25381200-25402400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:25382000-25402600	Weak transcription	Colonic Mucosa	Colon
37	chr12:25383000-25399000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:25384200-25392800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:25385200-25393600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:25385200-25402600	Weak transcription	Aorta	Aorta
41	chr12:25385400-25395400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:25386200-25392600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:25386200-25402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:25386400-25393400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:25386400-25402800	Weak transcription	Gastric	stomach
46	chr12:25386600-25393800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:25386600-25402600	Weak transcription	Fetal Kidney	kidney
48	chr12:25386800-25402600	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:25387000-25396800	Weak transcription	Hela-S3	cervix
50	chr12:25387600-25392000	Strong transcription	Primary B cells from peripheral blood	blood

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