Variant report

Variant	rs7617936
Chromosome Location	chr3:195040462-195040463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10439946	0.89[EUR][1000 genomes]
rs10439947	0.89[EUR][1000 genomes]
rs10439948	0.89[EUR][1000 genomes]
rs10439949	0.89[EUR][1000 genomes]
rs10933704	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11706218	0.90[EUR][1000 genomes]
rs11715185	0.81[AMR][1000 genomes]
rs11718226	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12054139	0.90[EUR][1000 genomes]
rs12054333	0.91[EUR][1000 genomes]
rs12054406	0.92[EUR][1000 genomes]
rs12629884	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630009	0.92[EUR][1000 genomes]
rs12636736	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13316914	0.84[EUR][1000 genomes]
rs13317705	0.89[EUR][1000 genomes]
rs13317782	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13320698	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13325966	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1353133	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1538768	0.89[EUR][1000 genomes]
rs1826584	0.89[EUR][1000 genomes]
rs1890853	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994880	0.89[EUR][1000 genomes]
rs1994881	0.89[EUR][1000 genomes]
rs2000052	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2029708	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2050806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066154	0.92[EUR][1000 genomes]
rs2131685	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275518	0.88[EUR][1000 genomes]
rs2275519	0.82[EUR][1000 genomes]
rs2410792	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677666	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4677668	0.92[EUR][1000 genomes]
rs4677669	0.90[EUR][1000 genomes]
rs4677826	0.90[EUR][1000 genomes]
rs4677827	0.90[EUR][1000 genomes]
rs4677828	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677829	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4677832	0.89[EUR][1000 genomes]
rs4677833	0.90[EUR][1000 genomes]
rs4677837	0.89[EUR][1000 genomes]
rs4677838	0.89[EUR][1000 genomes]
rs4677839	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677840	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4677842	0.89[EUR][1000 genomes]
rs4677843	0.89[EUR][1000 genomes]
rs4677844	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57760978	0.90[EUR][1000 genomes]
rs58067895	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58178384	0.89[EUR][1000 genomes]
rs59004692	0.84[EUR][1000 genomes]
rs59551685	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59563484	0.82[EUR][1000 genomes]
rs60100329	0.90[EUR][1000 genomes]
rs60177727	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62287061	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62287066	0.81[EUR][1000 genomes]
rs62287069	0.92[EUR][1000 genomes]
rs62287106	0.89[EUR][1000 genomes]
rs62287107	0.90[EUR][1000 genomes]
rs62287108	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62287109	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62287111	0.89[EUR][1000 genomes]
rs62287119	0.90[EUR][1000 genomes]
rs62288360	0.89[EUR][1000 genomes]
rs62288364	0.89[EUR][1000 genomes]
rs62288365	0.89[EUR][1000 genomes]
rs62288367	0.88[EUR][1000 genomes]
rs62288369	0.89[EUR][1000 genomes]
rs62288441	0.84[EUR][1000 genomes]
rs62288442	0.83[EUR][1000 genomes]
rs6437373	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6437375	0.89[EUR][1000 genomes]
rs6437376	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6437471	0.90[EUR][1000 genomes]
rs6763335	0.90[EUR][1000 genomes]
rs6763588	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6771771	0.89[EUR][1000 genomes]
rs6778652	0.84[EUR][1000 genomes]
rs6781311	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6785382	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6788868	0.84[EUR][1000 genomes]
rs6791563	0.84[EUR][1000 genomes]
rs6794216	0.89[EUR][1000 genomes]
rs6800221	0.83[EUR][1000 genomes]
rs6800562	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6801007	0.89[EUR][1000 genomes]
rs6801315	0.89[EUR][1000 genomes]
rs6801750	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803477	0.81[EUR][1000 genomes]
rs6803763	0.90[EUR][1000 genomes]
rs6806763	0.81[EUR][1000 genomes]
rs6806850	0.90[EUR][1000 genomes]
rs716898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73208931	0.83[EUR][1000 genomes]
rs7430205	0.90[EUR][1000 genomes]
rs7611090	0.88[EUR][1000 genomes]
rs7616598	0.89[EUR][1000 genomes]
rs7618499	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7621133	0.89[EUR][1000 genomes]
rs7623135	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627054	0.90[EUR][1000 genomes]
rs7627671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635603	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7635906	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7636824	0.89[EUR][1000 genomes]
rs7639146	0.90[EUR][1000 genomes]
rs7641810	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7650623	0.89[EUR][1000 genomes]
rs7652612	0.89[EUR][1000 genomes]
rs7653406	0.92[EUR][1000 genomes]
rs9288744	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288746	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9681021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809730	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9812506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9813425	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814214	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814344	0.88[EUR][1000 genomes]
rs9817672	0.89[EUR][1000 genomes]
rs9821765	0.84[EUR][1000 genomes]
rs9826999	0.89[EUR][1000 genomes]
rs9836665	0.89[EUR][1000 genomes]
rs9844354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9846555	0.88[EUR][1000 genomes]
rs9847544	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9848201	0.92[EUR][1000 genomes]
rs9848473	0.88[EUR][1000 genomes]
rs9854941	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9855453	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9859279	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859902	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9860798	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862710	0.89[EUR][1000 genomes]
rs9864603	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866537	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9868768	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870236	0.89[EUR][1000 genomes]
rs9876967	0.83[EUR][1000 genomes]
rs9879305	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv526569	chr3:195038287-195123495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7617936	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs7617936	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
4	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
5	chr3:195010000-195061000	Weak transcription	Fetal Kidney	kidney
6	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:195014200-195040800	Weak transcription	Hela-S3	cervix
8	chr3:195022600-195073400	Weak transcription	HMEC	breast
9	chr3:195022800-195073400	Weak transcription	NHEK	skin
10	chr3:195025400-195050600	Weak transcription	HSMMtube	muscle
11	chr3:195026800-195040600	Weak transcription	K562	blood
12	chr3:195026800-195051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:195029200-195046800	Weak transcription	NHDF-Ad	bronchial
14	chr3:195033000-195046800	Weak transcription	HSMM	muscle
15	chr3:195033800-195045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:195034800-195076800	Weak transcription	Psoas Muscle	Psoas
17	chr3:195038200-195041800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:195038600-195040600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:195038600-195040800	ZNF genes & repeats	Fetal Thymus	thymus
20	chr3:195038600-195041000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr3:195038600-195041000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:195038600-195041400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:195038600-195041400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:195038600-195041600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:195038600-195041600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:195038600-195041800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr3:195038600-195042000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr3:195038600-195042200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:195038600-195042200	Strong transcription	Primary T cells from cord blood	blood
30	chr3:195038600-195042600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:195038800-195043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:195039000-195041600	ZNF genes & repeats	GM12878-XiMat	blood
33	chr3:195039000-195042200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:195039200-195041000	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr3:195039200-195042200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr3:195039200-195042800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:195039200-195043200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:195039400-195041000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
39	chr3:195039400-195041000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:195039400-195041000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:195039400-195041000	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr3:195039400-195041400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:195039400-195041400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:195039400-195041600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr3:195039600-195040800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:195039600-195040800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:195039600-195040800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
48	chr3:195039600-195040800	ZNF genes & repeats	Ovary	ovary
49	chr3:195039600-195041000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:195039600-195041000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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