Variant report

Variant	rs6603962
Chromosome Location	chr1:92808487-92808488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10159094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10747503	0.80[ASN][1000 genomes]
rs10875319	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875349	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164226	0.90[ASN][1000 genomes]
rs11164288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164312	0.90[ASN][1000 genomes]
rs11164349	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164546	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11577572	1.00[JPT][hapmap]
rs11577839	0.90[ASN][1000 genomes]
rs11578012	0.90[ASN][1000 genomes]
rs11578400	0.90[ASN][1000 genomes]
rs11585255	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11586989	0.80[ASN][1000 genomes]
rs11588044	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11588153	1.00[JPT][hapmap]
rs11589858	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11803383	0.83[EUR][1000 genomes]
rs11803457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024731	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12086394	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094293	0.90[ASN][1000 genomes]
rs1226183	1.00[JPT][hapmap]
rs12401372	0.90[ASN][1000 genomes]
rs12404806	1.00[JPT][hapmap]
rs12407622	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12727665	0.90[ASN][1000 genomes]
rs12729867	1.00[JPT][hapmap]
rs12731923	0.90[ASN][1000 genomes]
rs12735898	0.90[ASN][1000 genomes]
rs12740246	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12755781	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12757533	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1483022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1487536	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487540	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17519972	1.00[JPT][hapmap]
rs1809606	0.90[ASN][1000 genomes]
rs1872007	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004814	0.90[ASN][1000 genomes]
rs2046620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087194	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391158	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2391161	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2391162	0.90[ASN][1000 genomes]
rs3103176	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118137	0.80[ASN][1000 genomes]
rs3122321	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122323	0.83[EUR][1000 genomes]
rs3122325	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3122327	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131813	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131820	0.96[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs3131827	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34090353	0.90[ASN][1000 genomes]
rs35580949	0.90[ASN][1000 genomes]
rs3929737	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393167	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414050	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658294	1.00[JPT][hapmap]
rs4658298	1.00[JPT][hapmap]
rs4658299	1.00[JPT][hapmap]
rs4658300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492164	1.00[JPT][hapmap]
rs4949888	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4970699	0.90[ASN][1000 genomes]
rs4970713	0.90[ASN][1000 genomes]
rs504606	1.00[JPT][hapmap]
rs515280	1.00[JPT][hapmap]
rs519932	1.00[JPT][hapmap]
rs556980	1.00[JPT][hapmap]
rs563113	1.00[JPT][hapmap]
rs569593	1.00[JPT][hapmap]
rs570368	1.00[JPT][hapmap]
rs6603971	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6604088	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604090	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662379	0.90[ASN][1000 genomes]
rs6663114	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6663118	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663905	0.90[ASN][1000 genomes]
rs6668803	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689366	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692287	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6702267	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720457	0.90[ASN][1000 genomes]
rs733012	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745793	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517541	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518974	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520275	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524120	0.90[ASN][1000 genomes]
rs7539757	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550680	0.90[ASN][1000 genomes]
rs7554154	0.83[EUR][1000 genomes]
rs912794	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439911	0.90[ASN][1000 genomes]
rs9440085	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9943178	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6603962	KIAA1107	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
2	chr1:92771800-92823800	Weak transcription	Colonic Mucosa	Colon
3	chr1:92789800-92812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:92790000-92815200	Weak transcription	Psoas Muscle	Psoas
6	chr1:92792400-92817400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:92792400-92823600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:92792600-92812400	Weak transcription	Right Ventricle	heart
9	chr1:92792600-92815000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:92792600-92846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:92792800-92850800	Weak transcription	Fetal Heart	heart
12	chr1:92793600-92817200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:92793600-92823400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:92793800-92811800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:92793800-92830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:92794000-92823000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:92795000-92817600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:92795000-92823000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:92795200-92815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:92795200-92817000	Weak transcription	Esophagus	oesophagus
21	chr1:92795200-92817000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:92795200-92823400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:92795200-92825000	Weak transcription	Aorta	Aorta
24	chr1:92795200-92825000	Weak transcription	Lung	lung
25	chr1:92795200-92830400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:92795200-92846600	Weak transcription	Gastric	stomach
27	chr1:92795200-92850200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:92795200-92851400	Weak transcription	Spleen	Spleen
29	chr1:92795400-92825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:92795600-92814400	Weak transcription	A549	lung
31	chr1:92795600-92825200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:92795600-92826400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:92795600-92831200	Weak transcription	NHLF	lung
34	chr1:92795800-92810800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:92795800-92817600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:92795800-92817800	Weak transcription	HSMMtube	muscle
37	chr1:92795800-92834800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:92796200-92817200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:92796400-92819600	Weak transcription	Pancreas	Pancrea
40	chr1:92796400-92823200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:92797800-92830800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:92798200-92846800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:92798600-92809000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:92799600-92830400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:92800200-92813800	Weak transcription	Hela-S3	cervix
46	chr1:92800200-92818400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:92800600-92809000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:92801600-92808800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:92801600-92813800	Weak transcription	NHDF-Ad	bronchial
50	chr1:92802600-92817400	Weak transcription	Fetal Brain Female	brain

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