Variant report

Variant	rs12593844
Chromosome Location	chr15:62247067-62247068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10468027	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10851704	0.83[CHB][hapmap];0.80[CHD][hapmap];0.89[LWK][hapmap];0.90[YRI][hapmap]
rs10851705	0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs11071634	0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.90[YRI][hapmap]
rs11071641	0.96[YRI][hapmap]
rs11630347	0.87[ASN][1000 genomes]
rs11631013	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11632842	0.83[JPT][hapmap]
rs11634516	0.86[YRI][hapmap]
rs11635569	0.80[EUR][1000 genomes]
rs11639147	0.87[ASN][1000 genomes]
rs11639482	0.81[CEU][hapmap]
rs12438431	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12439356	0.83[MEX][hapmap]
rs12439934	0.93[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12442212	0.83[MEX][hapmap]
rs12442675	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs12592402	0.81[CEU][hapmap]
rs12593860	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12708468	0.83[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs12898209	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap]
rs12899801	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901247	0.92[ASN][1000 genomes]
rs12901575	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs12902092	0.85[YRI][hapmap]
rs12908182	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909947	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910541	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912208	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]
rs1344601	0.85[CEU][hapmap]
rs1346035	0.87[ASN][1000 genomes]
rs1346037	0.87[ASN][1000 genomes]
rs1364810	0.93[YRI][hapmap]
rs1370177	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap]
rs1436958	0.91[GIH][hapmap]
rs1436965	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1436966	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs1561197	0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap]
rs17238252	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs17271158	0.88[ASN][1000 genomes]
rs17271235	0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17303968	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs17304010	0.82[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1991205	0.83[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap]
rs2042608	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2113932	0.96[YRI][hapmap]
rs2113933	0.96[YRI][hapmap]
rs2162062	0.81[CEU][hapmap]
rs2162064	0.82[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs2241491	0.83[CHB][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap]
rs28472272	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28587331	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28591222	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28725250	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3210522	0.83[CHB][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.90[YRI][hapmap]
rs3743294	0.90[YRI][hapmap]
rs3809517	0.93[LWK][hapmap]
rs3886246	0.83[JPT][hapmap];0.93[LWK][hapmap];0.86[YRI][hapmap]
rs4372632	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4541010	0.96[YRI][hapmap]
rs4581655	0.80[AFR][1000 genomes]
rs4587915	0.84[TSI][hapmap]
rs4620905	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs4638519	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4774425	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs4775442	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs4775444	0.83[JPT][hapmap];0.92[YRI][hapmap]
rs4775445	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4775447	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap]
rs6494299	0.86[YRI][hapmap]
rs6494300	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs7161883	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7163326	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap]
rs7163441	0.82[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.85[YRI][hapmap]
rs7164933	0.83[CHB][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap]
rs7166891	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7168164	0.82[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.80[YRI][hapmap]
rs7170293	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7172145	0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7178424	0.83[MEX][hapmap]
rs7178540	0.93[GIH][hapmap];0.83[MEX][hapmap]
rs731820	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs8023668	0.90[JPT][hapmap]
rs8029942	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]
rs8032433	0.91[GIH][hapmap]
rs8033816	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8037603	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs8038328	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs8039651	0.93[GIH][hapmap];0.82[MEX][hapmap]
rs933807	0.81[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs963024	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9788670	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 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	nsv569644	chr15:62202482-62247067	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12593844	TPM1	cis	cerebellum	SCAN
rs12593844	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
2	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
3	chr15:62185600-62262200	Weak transcription	Gastric	stomach
4	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
5	chr15:62185800-62300000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:62188600-62309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:62194600-62266800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr15:62195600-62285400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:62207800-62263200	Weak transcription	Fetal Brain Female	brain
10	chr15:62208200-62263200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:62208200-62290200	Weak transcription	Aorta	Aorta
12	chr15:62208400-62253200	Weak transcription	Thymus	Thymus
13	chr15:62209800-62250600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:62209800-62252400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:62214800-62250800	Weak transcription	NH-A	brain
16	chr15:62214800-62253600	Weak transcription	HepG2	liver
17	chr15:62214800-62265600	Weak transcription	Fetal Kidney	kidney
18	chr15:62219600-62253000	Weak transcription	Fetal Intestine Small	intestine
19	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:62221600-62253000	Weak transcription	Fetal Stomach	stomach
21	chr15:62222600-62253600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:62223400-62266600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:62228200-62255800	Weak transcription	HSMMtube	muscle
24	chr15:62229400-62280200	Weak transcription	K562	blood
25	chr15:62229800-62260800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:62230800-62317200	Weak transcription	Pancreas	Pancrea
27	chr15:62234200-62258600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:62234800-62257000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:62235600-62247600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:62235600-62277400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr15:62235800-62285000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:62236000-62255800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:62236000-62267000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:62236200-62267000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:62236600-62251600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:62236800-62251600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:62237200-62249200	Weak transcription	Hela-S3	cervix
38	chr15:62237200-62264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:62237400-62252000	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:62237400-62253000	Weak transcription	Left Ventricle	heart
41	chr15:62237400-62253800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:62237400-62255800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:62237400-62256200	Weak transcription	Colonic Mucosa	Colon
44	chr15:62237400-62262400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:62237400-62263400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:62237600-62247600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:62237600-62250200	Weak transcription	Fetal Brain Male	brain
48	chr15:62237600-62253800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:62237600-62253800	Weak transcription	Lung	lung
50	chr15:62237600-62262200	Weak transcription	Ovary	ovary

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