Variant report

Variant	rs8029942
Chromosome Location	chr15:62353458-62353459
allele	A/G
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	RCOR1	chr15:62351813-62353472	IMR90	lung:	n/a	n/a
2	GATA1	chr15:62351266-62353595	PBDE	blood:	n/a	n/a
3	RAD21	chr15:62351155-62353498	SK-N-SH	brain:	n/a	chr15:62352443-62352455 chr15:62352416-62352429 chr15:62352621-62352634
4	BHLHE40	chr15:62351886-62353472	GM12878	blood:	n/a	chr15:62352932-62352948 chr15:62352966-62352982
5	ZNF384	chr15:62353297-62353512	GM12878	blood:	n/a	n/a
6	CTCF	chr15:62351357-62353929	A549	lung:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
7	RUNX3	chr15:62351877-62353496	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:62351832-62353572	GM12878	blood:	n/a	n/a
9	HCFC1	chr15:62351216-62354024	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62352901..62356622-chr15:62357854..62362137,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-1	chr15:62353167-62353462	XLOC_011278
2	lnc-C2CD4A-1	chr15:62352713-62354633	ENSG00000259251.2
3	lnc-C2CD4A-1	chr15:62353167-62353473	ENSG00000259251.2

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

Extended variants
information (count: 125 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10047986	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1030859	0.86[AMR][1000 genomes];0.89[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];0.81[CHD][hapmap]
rs10851705	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11071634	0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs11071647	0.81[CEU][hapmap]
rs11071649	0.84[EUR][1000 genomes]
rs11629528	0.82[CEU][hapmap]
rs11629596	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11630347	0.98[ASN][1000 genomes]
rs11631013	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11632842	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs11633500	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11635977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11639147	0.98[ASN][1000 genomes]
rs11639482	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12438431	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12438690	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438803	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439356	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12439934	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12442212	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[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];1.00[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];0.80[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs12899801	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12900645	0.80[EUR][1000 genomes]
rs12901575	0.86[CHB][hapmap];0.83[JPT][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];0.86[ASN][1000 genomes]
rs12912208	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]
rs12913951	0.86[AMR][1000 genomes];0.89[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];0.81[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs1425270	0.85[CEU][hapmap]
rs1436958	0.91[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1436963	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1436964	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1436965	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1436966	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1561197	0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs17205407	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17205463	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17271235	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs17271403	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17271431	0.83[AMR][1000 genomes]
rs17271438	0.85[AMR][1000 genomes];0.86[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];0.80[EUR][1000 genomes]
rs2162064	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2414755	0.85[CEU][hapmap]
rs28542204	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28837073	0.82[EUR][1000 genomes]
rs3210522	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs34096515	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35123892	0.84[EUR][1000 genomes]
rs3743294	0.82[CEU][hapmap]
rs3784633	0.83[CEU][hapmap]
rs4143842	0.86[AMR][1000 genomes];0.88[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];0.82[ASN][1000 genomes]
rs4564516	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4587915	0.89[CEU][hapmap]
rs4638519	0.83[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4774425	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4775442	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4775444	0.83[JPT][hapmap]
rs4775445	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4775447	0.83[CHB][hapmap];0.81[CHD][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	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4775458	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6494300	0.90[JPT][hapmap]
rs7161883	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7162536	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7163326	0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs7163441	0.82[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7164933	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7166891	0.82[CEU][hapmap]
rs7168164	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs7170293	0.82[CEU][hapmap]
rs7177276	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7177711	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7178424	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7178540	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7178945	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs731820	0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8023668	0.90[JPT][hapmap]
rs8025877	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8026008	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8032433	0.81[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs8033816	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs8037603	0.82[JPT][hapmap]
rs8038932	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8039651	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs893156	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs893158	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs933807	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8029942	VPS13C	cis	cerebellum	SCAN
rs8029942	TPM1	cis	cerebellum	SCAN
rs8029942	TEX9	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62350800-62353600	Active TSS	NHDF-Ad	bronchial
2	chr15:62351000-62353600	Active TSS	Right Atrium	heart
3	chr15:62351000-62353800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:62351200-62353800	Active TSS	GM12878-XiMat	blood
5	chr15:62351400-62353600	Active TSS	Aorta	Aorta
6	chr15:62351400-62353600	Active TSS	Fetal Brain Male	brain
7	chr15:62351400-62353600	Active TSS	HSMMtube	muscle
8	chr15:62351400-62353800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:62351400-62354000	Active TSS	Primary T cells fromperipheralblood	blood
10	chr15:62351600-62353600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:62351600-62353600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:62351600-62353600	Active TSS	Brain Cingulate Gyrus	brain
13	chr15:62351600-62353600	Active TSS	Brain Hippocampus Middle	brain
14	chr15:62351600-62353600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:62351600-62353600	Active TSS	Colon Smooth Muscle	Colon
16	chr15:62351600-62353600	Active TSS	Fetal Thymus	thymus
17	chr15:62351600-62353800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:62351600-62353800	Active TSS	Brain Substantia Nigra	brain
19	chr15:62351600-62353800	Active TSS	Ovary	ovary
20	chr15:62351600-62354600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr15:62351800-62353600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:62351800-62353600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:62351800-62353600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr15:62351800-62353600	Active TSS	Rectal Smooth Muscle	rectum
25	chr15:62351800-62353600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr15:62351800-62353800	Active TSS	Brain Anterior Caudate	brain
27	chr15:62351800-62353800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr15:62351800-62353800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr15:62351800-62353800	Active TSS	Stomach Smooth Muscle	stomach
30	chr15:62351800-62354000	Active TSS	Thymus	Thymus
31	chr15:62352000-62353600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:62352000-62353800	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:62352000-62353800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:62352000-62353800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr15:62352000-62353800	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr15:62352000-62353800	Active TSS	Brain Angular Gyrus	brain
37	chr15:62352000-62353800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr15:62352200-62353800	Active TSS	Adipose Nuclei	Adipose
39	chr15:62352600-62353600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:62352600-62353600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:62352800-62353600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr15:62352800-62353600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:62352800-62353600	Flanking Active TSS	Liver	Liver
44	chr15:62352800-62353600	Flanking Active TSS	HUVEC	blood vessel
45	chr15:62352800-62353800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr15:62352800-62353800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr15:62352800-62354000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:62353000-62353600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:62353000-62353600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr15:62353000-62353600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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