Variant report

Variant	rs1394092
Chromosome Location	chr3:136196071-136196072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1070232	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs10935186	0.93[JPT][hapmap]
rs1145101	0.89[MEX][hapmap]
rs1145106	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs11715257	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717954	0.87[JPT][hapmap]
rs11919030	0.93[JPT][hapmap]
rs12330635	0.89[CHB][hapmap]
rs12489577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs12630999	0.86[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs12635723	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs12637102	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs1279425	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1279840	0.80[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs13068119	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs1711161	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1711170	0.86[JPT][hapmap]
rs1711171	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs17252498	0.83[MEX][hapmap]
rs1964675	0.88[AMR][1000 genomes]
rs2655008	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28478252	0.83[AMR][1000 genomes]
rs34602896	0.83[MEX][hapmap]
rs34967300	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs3821445	0.89[MEX][hapmap]
rs3856637	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs4521165	1.00[JPT][hapmap]
rs4678433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4678437	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs4678438	0.87[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs483465	0.90[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs595532	0.93[JPT][hapmap]
rs61789652	0.88[ASN][1000 genomes]
rs619605	0.93[JPT][hapmap]
rs6439646	0.81[EUR][1000 genomes]
rs6439649	1.00[JPT][hapmap]
rs650326	1.00[JPT][hapmap]
rs654237	0.93[JPT][hapmap]
rs655720	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs655836	0.93[JPT][hapmap]
rs667920	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs6789488	0.83[AMR][1000 genomes]
rs6791142	0.93[JPT][hapmap]
rs6791611	0.87[JPT][hapmap]
rs6794351	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6808312	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs695983	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs696081	1.00[JPT][hapmap]
rs696516	0.90[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap]
rs696517	0.94[MEX][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs699165	0.80[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs711975	0.93[JPT][hapmap]
rs711976	0.86[ASN][1000 genomes]
rs7432375	0.93[JPT][hapmap]
rs7618518	1.00[JPT][hapmap]
rs7621025	0.86[ASW][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs833752	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs900048	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289511	1.00[CHB][hapmap]
rs940174	0.93[JPT][hapmap]
rs9757777	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9759024	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9820485	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs9821478	0.89[CHB][hapmap]
rs9832056	1.00[CHB][hapmap]
rs9832813	1.00[CHB][hapmap]
rs9845762	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs9848883	0.89[CHB][hapmap]
rs9849696	0.88[ASN][1000 genomes]
rs9851986	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9854084	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9856769	0.89[CHB][hapmap]
rs9869720	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9883916	0.85[CEU][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1394092	NCK1	cis	parietal	SCAN
rs1394092	PCCB	cis	lymphoblastoid	seeQTL
rs1394092	MSL2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136196600	Weak transcription	HUVEC	blood vessel
3	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
8	chr3:136176600-136240000	Weak transcription	HMEC	breast
9	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:136176800-136205800	Weak transcription	Small Intestine	intestine
11	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
13	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:136177400-136198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
18	chr3:136179400-136204000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart
20	chr3:136181200-136205400	Weak transcription	Fetal Kidney	kidney
21	chr3:136181400-136211600	Weak transcription	A549	lung
22	chr3:136182000-136204400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:136183800-136212000	Weak transcription	Lung	lung
24	chr3:136189400-136196600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:136189800-136196600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:136189800-136196600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:136189800-136197200	Strong transcription	Dnd41	blood
28	chr3:136189800-136197600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:136190400-136196600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:136190400-136196600	Strong transcription	Primary T cells from cord blood	blood
31	chr3:136190600-136196200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:136190800-136196400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:136191000-136196600	Weak transcription	Gastric	stomach
34	chr3:136191000-136220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:136191400-136209400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:136192000-136196400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:136192000-136204000	Weak transcription	Fetal Stomach	stomach
39	chr3:136192200-136196800	Weak transcription	GM12878-XiMat	blood
40	chr3:136192200-136205400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:136192200-136212600	Weak transcription	Pancreas	Pancrea
42	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:136192400-136196800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:136192600-136206000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:136193400-136196200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:136193400-136196400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:136193800-136204800	Weak transcription	Fetal Brain Female	brain
49	chr3:136193800-136217200	Weak transcription	HepG2	liver
50	chr3:136193800-136231400	Weak transcription	NHLF	lung

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