Variant report

Variant	rs1353133
Chromosome Location	chr3:195160052-195160053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195159870..195162612-chr3:195162648..195164644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114331	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11706218	0.81[EUR][1000 genomes]
rs11718226	0.81[EUR][1000 genomes]
rs12054139	0.81[EUR][1000 genomes]
rs12629884	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13316914	0.86[EUR][1000 genomes]
rs13317782	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320698	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826584	0.82[EUR][1000 genomes]
rs1890853	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1994880	0.82[EUR][1000 genomes]
rs1994881	0.82[EUR][1000 genomes]
rs2029708	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050806	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2131685	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275518	0.81[EUR][1000 genomes]
rs2410792	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677669	0.81[EUR][1000 genomes]
rs4677826	0.81[EUR][1000 genomes]
rs4677827	0.81[EUR][1000 genomes]
rs4677828	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4677833	0.81[EUR][1000 genomes]
rs4677837	0.82[EUR][1000 genomes]
rs4677838	0.82[EUR][1000 genomes]
rs4677839	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677840	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677842	0.82[EUR][1000 genomes]
rs4677843	0.82[EUR][1000 genomes]
rs4677844	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57760978	0.81[EUR][1000 genomes]
rs58067895	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58178384	0.82[EUR][1000 genomes]
rs59004692	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs59551685	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60100329	0.81[EUR][1000 genomes]
rs62287107	0.81[EUR][1000 genomes]
rs62287108	0.81[EUR][1000 genomes]
rs62287119	0.81[EUR][1000 genomes]
rs62288364	0.82[EUR][1000 genomes]
rs62288365	0.82[EUR][1000 genomes]
rs62288367	0.81[EUR][1000 genomes]
rs62288369	0.82[EUR][1000 genomes]
rs62288441	0.86[EUR][1000 genomes]
rs62288442	0.88[EUR][1000 genomes]
rs6437376	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6437471	0.81[EUR][1000 genomes]
rs6763335	0.81[EUR][1000 genomes]
rs6763588	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6778652	0.86[EUR][1000 genomes]
rs6781311	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6785382	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788868	0.86[EUR][1000 genomes]
rs6791563	0.86[EUR][1000 genomes]
rs6800221	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6800562	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6801007	0.82[EUR][1000 genomes]
rs6801750	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803477	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6803763	0.81[EUR][1000 genomes]
rs6806850	0.81[EUR][1000 genomes]
rs716898	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73208931	0.88[EUR][1000 genomes]
rs7430205	0.81[EUR][1000 genomes]
rs7616598	0.82[EUR][1000 genomes]
rs7617936	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618499	0.81[EUR][1000 genomes]
rs7621133	0.82[EUR][1000 genomes]
rs7623135	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627054	0.81[EUR][1000 genomes]
rs7627671	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7635603	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639146	0.81[EUR][1000 genomes]
rs7641810	0.81[EUR][1000 genomes]
rs9288744	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288746	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9681021	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809730	0.81[EUR][1000 genomes]
rs9812506	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813425	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9814214	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814344	0.81[EUR][1000 genomes]
rs9817672	0.82[EUR][1000 genomes]
rs9821765	0.86[EUR][1000 genomes]
rs9826999	0.82[EUR][1000 genomes]
rs9836665	0.82[EUR][1000 genomes]
rs9840309	0.83[ASN][1000 genomes]
rs9844354	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9846555	0.81[EUR][1000 genomes]
rs9847544	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848201	0.82[EUR][1000 genomes]
rs9848473	0.81[EUR][1000 genomes]
rs9859279	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9859822	0.83[ASN][1000 genomes]
rs9860798	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864603	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9866537	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868768	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9870236	0.82[EUR][1000 genomes]
rs9876967	0.88[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
10	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
11	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
12	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription 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	54 gene(s)	inside rSNPs	diseases
13	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
15	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
17	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1353133	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs1353133	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195094800-195161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:195095200-195161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:195131800-195160600	Weak transcription	Hela-S3	cervix
4	chr3:195132000-195161200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:195133800-195161000	Weak transcription	NHDF-Ad	bronchial
6	chr3:195144800-195161200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:195145600-195162400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:195147000-195161000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:195147000-195162200	Weak transcription	Esophagus	oesophagus
10	chr3:195147200-195161800	Weak transcription	Fetal Thymus	thymus
11	chr3:195147800-195160400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:195147800-195162400	Weak transcription	Left Ventricle	heart
13	chr3:195148600-195161000	Weak transcription	K562	blood
14	chr3:195148600-195161800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:195150600-195161000	Weak transcription	NHLF	lung
16	chr3:195153400-195160600	Weak transcription	Primary T cells from cord blood	blood
17	chr3:195153600-195161000	Weak transcription	Fetal Lung	lung
18	chr3:195154000-195161000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:195155200-195161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:195155200-195161200	Weak transcription	Thymus	Thymus
21	chr3:195155200-195162000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:195155200-195162000	Weak transcription	Fetal Stomach	stomach
23	chr3:195157400-195162000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:195157600-195160800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:195157600-195162000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:195158000-195161000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:195158200-195160600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:195158400-195160600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:195158400-195161000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:195159000-195161000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:195159000-195161800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:195159000-195161800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:195159000-195161800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:195159200-195160200	Enhancers	Ovary	ovary
35	chr3:195159200-195161000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:195159200-195161200	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:195159200-195161800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:195159400-195160200	Enhancers	Lung	lung
39	chr3:195159400-195160600	Enhancers	Primary B cells from cord blood	blood
40	chr3:195159400-195160600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:195159400-195162000	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:195159400-195162000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:195159600-195160200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:195159600-195160200	Enhancers	Psoas Muscle	Psoas
45	chr3:195159600-195160600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:195159600-195160600	Weak transcription	Dnd41	blood
47	chr3:195159600-195160800	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:195159600-195160800	Weak transcription	A549	lung
49	chr3:195159600-195161000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:195159600-195161800	Weak transcription	HMEC	breast

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