Variant report

Variant	rs3784635
Chromosome Location	chr15:62254989-62254990
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	FAM48A	chr15:62254939-62255081	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
VPS13C	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10519144	0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519154	0.83[ASN][1000 genomes]
rs12232347	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438629	0.86[GIH][hapmap];1.00[TSI][hapmap]
rs12439027	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439366	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440611	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12440748	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441358	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441436	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12441791	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12442506	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12442569	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12591667	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594218	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12594396	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595158	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1364809	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1559673	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17238110	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17238127	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17238189	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17238210	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303831	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17303866	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17303873	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2113935	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs34516157	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35057371	0.87[ASN][1000 genomes]
rs35592904	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36143406	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809516	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774426	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775446	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775452	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775456	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7177538	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747848	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72747849	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72747852	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72747853	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72747855	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747856	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747868	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72747869	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747870	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747874	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747879	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747895	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747896	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747901	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749703	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749733	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72749742	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72749744	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749754	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72749772	0.86[ASN][1000 genomes]
rs8030161	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033347	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs963023	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9635356	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788653	0.86[EUR][1000 genomes]
rs9788739	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv516639	chr15:62175134-62340126	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	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
10	nsv904291	chr15:62178695-62287456	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv904292	chr15:62178695-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv904293	chr15:62178695-62338797	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv904295	chr15:62198564-62259637	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv904296	chr15:62198564-62313373	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	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
19	nsv904297	chr15:62202482-62313373	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv569645	chr15:62202482-62319307	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	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
22	esv1816724	chr15:62205104-62285146	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv569647	chr15:62214607-62284101	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv904298	chr15:62218689-62338797	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	nsv569648	chr15:62239697-62340126	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
26	nsv457177	chr15:62243197-62301094	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv569649	chr15:62243197-62301094	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	nsv569650	chr15:62243197-62313373	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	nsv569651	chr15:62243197-62313417	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
2	chr15:62185600-62262200	Weak transcription	Gastric	stomach
3	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
4	chr15:62185800-62300000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:62188600-62309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:62194600-62266800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:62195600-62285400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:62207800-62263200	Weak transcription	Fetal Brain Female	brain
9	chr15:62208200-62263200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:62208200-62290200	Weak transcription	Aorta	Aorta
11	chr15:62214800-62265600	Weak transcription	Fetal Kidney	kidney
12	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:62223400-62266600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:62228200-62255800	Weak transcription	HSMMtube	muscle
15	chr15:62229400-62280200	Weak transcription	K562	blood
16	chr15:62229800-62260800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:62230800-62317200	Weak transcription	Pancreas	Pancrea
18	chr15:62234200-62258600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:62234800-62257000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:62235600-62277400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:62235800-62285000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:62236000-62255800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:62236000-62267000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:62236200-62267000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:62237200-62264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:62237400-62255800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:62237400-62256200	Weak transcription	Colonic Mucosa	Colon
28	chr15:62237400-62262400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:62237400-62263400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:62237600-62262200	Weak transcription	Ovary	ovary
31	chr15:62237600-62266200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:62237600-62266600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:62238000-62262200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:62239400-62256800	Weak transcription	NHEK	skin
35	chr15:62239400-62266200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr15:62239600-62262200	Weak transcription	NHLF	lung
37	chr15:62242200-62262200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:62242400-62266400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:62242800-62255800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:62243200-62257000	Weak transcription	Brain Germinal Matrix	brain
41	chr15:62243800-62259600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:62244200-62260200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
44	chr15:62244800-62263800	Weak transcription	Stomach Mucosa	stomach
45	chr15:62244800-62266800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:62244800-62278600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:62245000-62257800	Weak transcription	Brain Substantia Nigra	brain
48	chr15:62245000-62266800	Weak transcription	Fetal Heart	heart
49	chr15:62245200-62258600	Weak transcription	Brain Angular Gyrus	brain
50	chr15:62245800-62260400	Strong transcription	Liver	Liver

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