Variant report

Variant	rs11632842
Chromosome Location	chr15:62329868-62329869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62328623..62331543-chr15:62331564..62333336,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10468027	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519153	0.82[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10851704	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs10851705	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11071634	0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11071635	0.95[JPT][hapmap]
rs11071639	0.83[ASN][1000 genomes]
rs11071641	0.95[JPT][hapmap]
rs11071647	0.95[JPT][hapmap]
rs11071648	0.83[AMR][1000 genomes]
rs11071650	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11629528	0.82[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs11630347	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11630353	0.82[EUR][1000 genomes]
rs11631013	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11634516	0.95[JPT][hapmap];0.86[MEX][hapmap]
rs11634693	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11635621	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11638793	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11639147	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12438431	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12442448	0.85[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12591155	0.85[CEU][hapmap]
rs12591593	0.82[EUR][1000 genomes]
rs12592464	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593844	0.83[JPT][hapmap]
rs12593860	0.86[ASN][1000 genomes]
rs12595300	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12708468	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12898209	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899801	0.83[JPT][hapmap]
rs12901575	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902092	0.95[JPT][hapmap]
rs12903649	0.80[EUR][1000 genomes]
rs12910541	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12912208	0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs12917535	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1364810	0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs1370177	0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1436959	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs1436961	0.80[AMR][1000 genomes]
rs1436965	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436966	0.83[JPT][hapmap]
rs1534542	0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs1561197	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17238252	0.95[JPT][hapmap]
rs17271235	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17303968	0.95[JPT][hapmap]
rs17304010	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1991205	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2042610	0.95[JPT][hapmap]
rs2113932	0.95[JPT][hapmap]
rs2113933	0.95[JPT][hapmap]
rs2162064	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241491	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2414756	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2414758	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28472272	0.86[ASN][1000 genomes]
rs28587331	0.87[ASN][1000 genomes]
rs28591222	0.86[ASN][1000 genomes]
rs28725250	0.86[ASN][1000 genomes]
rs2899678	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3210522	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs3743294	0.91[JPT][hapmap]
rs3784445	0.89[GIH][hapmap]
rs3809517	0.85[TSI][hapmap]
rs3886246	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4372632	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4541010	0.95[JPT][hapmap]
rs4620905	0.95[JPT][hapmap]
rs4638519	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774425	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4775442	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4775444	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4775445	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4775447	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6494299	0.95[JPT][hapmap]
rs6494300	0.95[JPT][hapmap]
rs7161883	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163326	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs7163441	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7164933	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7168164	0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8023668	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8025404	0.81[EUR][1000 genomes]
rs8029942	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs8033816	0.83[JPT][hapmap]
rs8037603	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8038328	0.91[JPT][hapmap]
rs9788670	0.95[JPT][hapmap]
rs9920758	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs9989353	0.80[AMR][1000 genomes]
rs9989354	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	esv3450900	chr15:62328660-62330708	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3355515	chr15:62329060-62330258	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11632842	TEX9	cis	cerebellum	SCAN
rs11632842	TEX9	cis	parietal	SCAN
rs11632842	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
2	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
3	chr15:62265600-62338200	Weak transcription	Stomach Mucosa	stomach
4	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:62288600-62336600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:62300000-62334600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:62300600-62330600	Weak transcription	Aorta	Aorta
9	chr15:62300600-62330600	Weak transcription	Fetal Intestine Small	intestine
10	chr15:62300600-62337600	Weak transcription	Fetal Stomach	stomach
11	chr15:62300600-62342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:62300600-62345800	Weak transcription	Gastric	stomach
13	chr15:62300600-62351800	Weak transcription	Lung	lung
14	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:62301600-62334400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:62301600-62336000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
18	chr15:62302200-62351600	Weak transcription	Ovary	ovary
19	chr15:62302400-62336200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:62302800-62333200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:62306200-62343600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:62313400-62335400	Weak transcription	Fetal Kidney	kidney
23	chr15:62313400-62337000	Weak transcription	Placenta	Placenta
24	chr15:62313400-62342800	Weak transcription	Left Ventricle	heart
25	chr15:62313400-62345600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:62313600-62332600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:62314800-62338000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:62315000-62330400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:62315200-62334200	Weak transcription	Fetal Lung	lung
30	chr15:62315200-62338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:62315200-62342600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:62320000-62336600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:62320600-62335400	Weak transcription	Fetal Intestine Large	intestine
34	chr15:62321200-62350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:62322600-62333000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:62322800-62332000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:62322800-62332000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:62322800-62338600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:62323000-62330200	Weak transcription	Liver	Liver
40	chr15:62323000-62330600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:62323400-62332200	Weak transcription	Adipose Nuclei	Adipose
42	chr15:62323600-62333200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:62325800-62332200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr15:62326000-62330200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:62326000-62332000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:62326200-62332200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:62326200-62337800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:62326600-62337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:62327000-62331800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:62327400-62332200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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