Variant report

Variant	rs12912208
Chromosome Location	chr15:62354570-62354571
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	FOS	chr15:62354510-62354592	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr15:62354510-62354631	MCF10A-Er-Src	breast:	n/a	n/a
3	MAFK	chr15:62354566-62354877	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62353762..62355861-chr15:62356925..62359258,2	MCF-7	breast:
2	chr15:62352901..62356622-chr15:62357854..62362137,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-1	chr15:62352713-62354633	ENSG00000259251.2

Variant related genes	Relation type
VPS13C	TF binding region
C2CD4A	TF binding region
ENSG00000198535	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10047986	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1030859	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10468026	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10468027	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10519153	0.82[CEU][hapmap]
rs10851704	0.83[CHB][hapmap];0.80[YRI][hapmap]
rs10851705	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11071634	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap]
rs11071647	0.81[CEU][hapmap];0.83[YRI][hapmap]
rs11071649	0.84[EUR][1000 genomes]
rs11629528	0.82[CEU][hapmap];0.80[YRI][hapmap]
rs11629596	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11630347	0.98[ASN][1000 genomes]
rs11631013	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11632842	0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs11633500	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11635977	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639147	0.98[ASN][1000 genomes]
rs11639482	0.85[CEU][hapmap]
rs12438431	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12438690	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438803	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12439356	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439934	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs12442212	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442675	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12592402	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12592464	0.80[ASN][1000 genomes]
rs12593844	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12594658	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12594946	0.82[EUR][1000 genomes]
rs12708468	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12898209	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs12899801	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12901575	0.86[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs12908081	0.85[CEU][hapmap]
rs12909947	0.86[ASN][1000 genomes]
rs12910541	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12913951	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13379947	0.85[CEU][hapmap]
rs1344601	0.85[CEU][hapmap]
rs1364810	0.82[CEU][hapmap]
rs1370177	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap]
rs1425270	0.85[CEU][hapmap]
rs1436958	0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs1436963	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436964	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436965	0.83[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap]
rs1436966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534542	0.96[YRI][hapmap]
rs1561197	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.93[YRI][hapmap]
rs17205407	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17205463	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17271235	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs17271403	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17271431	0.85[AMR][1000 genomes]
rs17271438	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17303968	0.82[JPT][hapmap]
rs17304010	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1981916	0.85[CEU][hapmap]
rs2042608	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2042610	0.82[CEU][hapmap]
rs2162062	0.85[CEU][hapmap]
rs2162064	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap]
rs2414755	0.85[CEU][hapmap]
rs28542204	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28837073	0.82[EUR][1000 genomes]
rs3210522	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap]
rs34096515	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35123892	0.84[EUR][1000 genomes]
rs3743294	0.82[CEU][hapmap];0.80[YRI][hapmap]
rs3784633	0.83[CEU][hapmap]
rs4143842	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4143843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4372632	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs4564516	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4587915	0.89[CEU][hapmap]
rs4638519	0.83[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs4774425	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4775444	0.83[JPT][hapmap]
rs4775445	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4775447	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4775453	0.85[CEU][hapmap]
rs4775455	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775457	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775458	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6494300	0.90[JPT][hapmap];0.80[YRI][hapmap]
rs7161883	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs7162536	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7163326	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs7163441	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7164933	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap]
rs7166891	0.82[CEU][hapmap]
rs7168164	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap]
rs7170293	0.82[CEU][hapmap]
rs7177276	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7177711	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7178424	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7178540	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7178945	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731820	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8023668	0.90[JPT][hapmap]
rs8025877	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8026008	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8029942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032433	0.81[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs8033816	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs8037603	0.82[JPT][hapmap]
rs8038932	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8039651	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs893156	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs893158	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs933807	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12912208	TPM1	cis	cerebellum	SCAN
rs12912208	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62351600-62354600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr15:62353400-62355200	Weak transcription	Hela-S3	cervix
3	chr15:62353400-62355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:62353400-62355600	Weak transcription	Gastric	stomach
5	chr15:62353400-62355600	Weak transcription	Pancreas	Pancrea
6	chr15:62353400-62355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:62353400-62355800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:62353400-62356000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:62353400-62358800	Weak transcription	Placenta	Placenta
10	chr15:62353400-62358800	Weak transcription	Psoas Muscle	Psoas
11	chr15:62353400-62358800	Weak transcription	Stomach Mucosa	stomach
12	chr15:62353400-62359000	Weak transcription	Lung	lung
13	chr15:62353600-62354600	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:62353600-62355400	Weak transcription	HMEC	breast
15	chr15:62353600-62355400	Weak transcription	NHEK	skin
16	chr15:62353600-62355600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:62353600-62355800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:62353600-62356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:62353600-62356400	Weak transcription	K562	blood
20	chr15:62353600-62358400	Weak transcription	Aorta	Aorta
21	chr15:62353600-62358600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:62353600-62358800	Weak transcription	Liver	Liver
23	chr15:62353600-62358800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:62353600-62358800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:62353600-62358800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:62353800-62354600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:62353800-62354600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr15:62353800-62358800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:62354000-62354600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:62354000-62354800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:62354000-62358600	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:62354000-62358800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:62354200-62354600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr15:62354200-62354600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:62354200-62354600	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr15:62354200-62358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:62354200-62358800	Weak transcription	Brain Anterior Caudate	brain
38	chr15:62354400-62354600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr15:62354400-62354600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr15:62354400-62355600	Weak transcription	Fetal Intestine Small	intestine
41	chr15:62354400-62358600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:62354400-62358600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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