Variant report

Variant	rs11715202
Chromosome Location	chr3:194986149-194986150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194978258..194982064-chr3:194982349..194986625,5	MCF-7	breast:
2	chr3:194986029..194989766-chr3:194990279..194993841,6	K562	blood:
3	chr3:194985883..194988240-chr3:195267670..195269662,2	K562	blood:
4	chr3:194384423..194386618-chr3:194984770..194986296,2	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10439946	0.85[ASN][1000 genomes]
rs10439947	0.85[ASN][1000 genomes]
rs10439948	0.81[ASN][1000 genomes]
rs10439949	0.85[ASN][1000 genomes]
rs10933704	0.86[EUR][1000 genomes]
rs11706218	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11709417	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715185	0.83[EUR][1000 genomes]
rs11718226	0.85[ASN][1000 genomes]
rs12054139	0.84[ASN][1000 genomes]
rs12054333	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12054406	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12630009	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12636736	0.85[ASN][1000 genomes]
rs13317705	0.84[ASN][1000 genomes]
rs13325966	0.82[ASN][1000 genomes]
rs1538768	0.85[ASN][1000 genomes]
rs1826584	0.84[ASN][1000 genomes]
rs1994880	0.81[ASN][1000 genomes]
rs1994881	0.82[ASN][1000 genomes]
rs2000051	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2000052	0.81[EUR][1000 genomes]
rs2066154	0.87[ASN][1000 genomes]
rs2275518	0.85[ASN][1000 genomes]
rs2275519	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2410804	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4461369	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677666	0.86[EUR][1000 genomes]
rs4677668	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4677669	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4677826	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4677827	0.84[AFR][1000 genomes]
rs4677829	0.87[ASN][1000 genomes]
rs4677832	0.85[ASN][1000 genomes]
rs4677833	0.84[ASN][1000 genomes]
rs4677837	0.85[ASN][1000 genomes]
rs4677838	0.85[ASN][1000 genomes]
rs4677842	0.82[ASN][1000 genomes]
rs4677843	0.82[ASN][1000 genomes]
rs57124286	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57760978	0.84[ASN][1000 genomes]
rs58178384	0.82[ASN][1000 genomes]
rs59563484	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60042817	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60100329	0.85[ASN][1000 genomes]
rs60177727	0.85[ASN][1000 genomes]
rs62285259	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62287066	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62287069	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62287106	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62287107	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62287108	0.87[ASN][1000 genomes]
rs62287109	0.87[ASN][1000 genomes]
rs62287111	0.85[ASN][1000 genomes]
rs62287119	0.85[ASN][1000 genomes]
rs62288360	0.84[ASN][1000 genomes]
rs62288364	0.82[ASN][1000 genomes]
rs62288365	0.85[ASN][1000 genomes]
rs62288367	0.84[ASN][1000 genomes]
rs62288369	0.82[ASN][1000 genomes]
rs6437373	0.85[ASN][1000 genomes]
rs6437375	0.84[ASN][1000 genomes]
rs6437471	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6763335	0.85[ASN][1000 genomes]
rs6771771	0.85[ASN][1000 genomes]
rs6794216	0.84[ASN][1000 genomes]
rs6801007	0.85[ASN][1000 genomes]
rs6801315	0.85[ASN][1000 genomes]
rs6803763	0.85[ASN][1000 genomes]
rs6806850	0.85[ASN][1000 genomes]
rs7430205	0.84[ASN][1000 genomes]
rs7611090	0.81[ASN][1000 genomes]
rs7616598	0.84[ASN][1000 genomes]
rs7618499	0.85[ASN][1000 genomes]
rs7621133	0.82[ASN][1000 genomes]
rs7622180	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627054	0.84[ASN][1000 genomes]
rs7632534	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635906	0.83[ASN][1000 genomes]
rs7636824	0.83[ASN][1000 genomes]
rs7639146	0.84[ASN][1000 genomes]
rs7641810	0.87[ASN][1000 genomes]
rs7650623	0.84[ASN][1000 genomes]
rs7652612	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7653406	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9790153	0.81[ASN][1000 genomes]
rs9809730	0.85[ASN][1000 genomes]
rs9814344	0.81[ASN][1000 genomes]
rs9817672	0.83[ASN][1000 genomes]
rs9826999	0.84[ASN][1000 genomes]
rs9836665	0.85[ASN][1000 genomes]
rs9846555	0.85[ASN][1000 genomes]
rs9848201	0.81[ASN][1000 genomes]
rs9848473	0.84[ASN][1000 genomes]
rs9854941	0.85[ASN][1000 genomes]
rs9855453	0.85[ASN][1000 genomes]
rs9859902	0.83[ASN][1000 genomes]
rs9862710	0.85[ASN][1000 genomes]
rs9870236	0.82[ASN][1000 genomes]
rs9879305	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11715202	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs11715202	XXYLT1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981400-194987800	Weak transcription	Psoas Muscle	Psoas
2	chr3:194981400-194990000	Weak transcription	HSMMtube	muscle
3	chr3:194981400-194990800	Weak transcription	Aorta	Aorta
4	chr3:194981600-194986200	Weak transcription	Hela-S3	cervix
5	chr3:194981600-194986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:194981600-194986400	Weak transcription	Left Ventricle	heart
7	chr3:194981600-194986400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:194981600-194986800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:194981600-194987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:194981600-194989600	Weak transcription	Right Ventricle	heart
11	chr3:194981600-194989800	Weak transcription	Brain Substantia Nigra	brain
12	chr3:194981600-194990000	Weak transcription	A549	lung
13	chr3:194981600-194990200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:194981600-194990200	Weak transcription	HSMM	muscle
15	chr3:194981600-194990600	Weak transcription	Ovary	ovary
16	chr3:194981800-194986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:194981800-194986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:194981800-194986200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:194981800-194986200	Weak transcription	NHLF	lung
20	chr3:194981800-194986400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:194981800-194986600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:194981800-194986600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:194981800-194986800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:194981800-194987200	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:194981800-194987400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:194981800-194987800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:194981800-194987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:194981800-194987800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:194981800-194989400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:194981800-194989400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:194981800-194989400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:194981800-194989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:194981800-194989600	Weak transcription	Liver	Liver
34	chr3:194981800-194989600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:194981800-194989600	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:194981800-194989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:194981800-194989600	Weak transcription	Fetal Heart	heart
38	chr3:194981800-194989600	Weak transcription	Lung	lung
39	chr3:194981800-194989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:194981800-194989800	Weak transcription	Adipose Nuclei	Adipose
41	chr3:194981800-194989800	Weak transcription	Colonic Mucosa	Colon
42	chr3:194981800-194989800	Weak transcription	Fetal Brain Female	brain
43	chr3:194981800-194989800	Weak transcription	Gastric	stomach
44	chr3:194981800-194989800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:194981800-194989800	Weak transcription	NHDF-Ad	bronchial
46	chr3:194981800-194990000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:194981800-194990000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:194981800-194990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:194981800-194990000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:194981800-194990000	Weak transcription	Brain Anterior Caudate	brain

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