Variant report

Variant	rs667920
Chromosome Location	chr3:136069472-136069473
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1070232	1.00[JPT][hapmap]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs1145101	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs1145106	0.85[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.86[JPT][hapmap]
rs11715257	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs11717954	0.87[JPT][hapmap]
rs12330258	0.87[ASN][1000 genomes]
rs12330635	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs1279086	1.00[JPT][hapmap]
rs1279425	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1279840	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1291921	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13068119	0.88[MEX][hapmap]
rs1394092	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs1618069	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1711161	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1711170	0.86[JPT][hapmap]
rs1711171	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17252498	0.88[MEX][hapmap]
rs1964675	0.81[ASN][1000 genomes]
rs2655008	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs28478252	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34967300	0.88[MEX][hapmap]
rs3755636	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3821445	0.94[MEX][hapmap]
rs3957816	0.86[JPT][hapmap]
rs4678428	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4678433	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs483465	0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs548288	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576771	0.92[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs619605	0.93[JPT][hapmap]
rs632016	0.81[ASN][1000 genomes]
rs645040	0.86[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap]
rs650326	1.00[JPT][hapmap]
rs650505	0.83[ASN][1000 genomes]
rs654237	0.93[JPT][hapmap]
rs655720	0.87[ASN][1000 genomes]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs665200	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770476	0.93[ASN][1000 genomes]
rs6789488	0.83[ASN][1000 genomes]
rs6791611	0.87[JPT][hapmap]
rs684773	0.86[JPT][hapmap];0.88[MEX][hapmap]
rs687339	0.86[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs695983	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs696081	1.00[JPT][hapmap]
rs696516	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs696517	1.00[MEX][hapmap];0.81[YRI][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs699165	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs711975	0.93[JPT][hapmap]
rs72493178	0.83[ASN][1000 genomes]
rs73222262	0.81[ASN][1000 genomes]
rs7372313	0.86[JPT][hapmap]
rs7628146	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7644541	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8045	0.83[MEX][hapmap]
rs833752	0.89[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895894	0.86[JPT][hapmap]
rs900048	1.00[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap]
rs9289511	1.00[CHB][hapmap]
rs9809427	0.89[ASN][1000 genomes]
rs9820485	1.00[CHB][hapmap]
rs9832056	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9832556	0.85[ASN][1000 genomes]
rs9832813	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs9845457	0.86[JPT][hapmap]
rs9848883	0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs9851986	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs9854084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9854328	0.88[ASN][1000 genomes]
rs9856769	0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs9869720	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs9883916	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak 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 target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs667920	MSL2	cis	cerebellum	SCAN
rs667920	NCK1	cis	parietal	SCAN
rs667920	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:136042600-136072600	Strong transcription	Dnd41	blood
4	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
5	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:136052800-136070800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:136053000-136072400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:136054200-136085400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:136054600-136074200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:136054800-136076600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:136055600-136073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
20	chr3:136057800-136069800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:136059000-136072000	Weak transcription	GM12878-XiMat	blood
22	chr3:136059600-136070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:136059600-136079000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:136061800-136074200	Weak transcription	Brain Germinal Matrix	brain
25	chr3:136063200-136071000	Weak transcription	Fetal Brain Female	brain
26	chr3:136063200-136072200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:136063400-136071800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:136063400-136072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:136063400-136072200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:136063400-136073800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:136063600-136097000	Weak transcription	Colonic Mucosa	Colon
34	chr3:136063600-136105600	Weak transcription	Gastric	stomach
35	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
36	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
37	chr3:136063800-136072200	Weak transcription	Stomach Mucosa	stomach
38	chr3:136063800-136095200	Weak transcription	Lung	lung
39	chr3:136064800-136069600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr3:136064800-136072400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:136065400-136097200	Weak transcription	HepG2	liver
42	chr3:136066200-136069800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:136066400-136069800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:136066600-136069800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:136066800-136069800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:136067200-136071200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:136067400-136070000	Strong transcription	Primary T cells from cord blood	blood
48	chr3:136067400-136070800	Strong transcription	Fetal Thymus	thymus
49	chr3:136067600-136074600	Weak transcription	Fetal Intestine Large	intestine
50	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel

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