Variant report

Variant	rs12740246
Chromosome Location	chr1:92805222-92805223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10159094	1.00[JPT][hapmap]
rs10874637	0.88[EUR][1000 genomes]
rs10875319	1.00[JPT][hapmap]
rs10875349	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11164226	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164288	1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs11164312	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11164546	0.80[ASN][1000 genomes]
rs11577572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11577839	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11578012	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11578400	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580693	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581176	1.00[CHB][hapmap]
rs11585255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11586355	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11586989	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11588044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11588153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11589858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11803457	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12024731	0.80[ASN][1000 genomes]
rs12086394	0.80[ASN][1000 genomes]
rs12094293	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1226183	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12401372	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12404806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12406749	0.83[EUR][1000 genomes]
rs12407622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12411162	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12724638	0.82[CEU][hapmap]
rs12727665	0.90[ASN][1000 genomes]
rs12729867	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731923	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12734478	0.91[CEU][hapmap]
rs12735898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12749317	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12755781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12757533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759512	0.83[EUR][1000 genomes]
rs1384612	0.83[EUR][1000 genomes]
rs1384613	0.83[EUR][1000 genomes]
rs1483022	1.00[JPT][hapmap]
rs1487536	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1487540	1.00[JPT][hapmap]
rs1542685	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17519385	0.84[EUR][1000 genomes]
rs17519972	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17578686	0.84[EUR][1000 genomes]
rs1809606	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1872007	1.00[JPT][hapmap]
rs2004814	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2046620	1.00[JPT][hapmap]
rs2069051	0.84[EUR][1000 genomes]
rs2087194	1.00[JPT][hapmap]
rs2391158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391162	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893200	1.00[JPT][hapmap]
rs3103176	1.00[JPT][hapmap]
rs3103178	1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs3103181	1.00[JPT][hapmap]
rs3131814	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3131828	1.00[JPT][hapmap]
rs34090353	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35015161	0.81[EUR][1000 genomes]
rs35580949	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3929737	0.80[ASN][1000 genomes]
rs4393167	0.80[ASN][1000 genomes]
rs4414050	0.80[ASN][1000 genomes]
rs4658294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4658297	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4658298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4658299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4658300	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs492164	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4949888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970699	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970713	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs504606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs511546	1.00[JPT][hapmap]
rs515280	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs519932	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs556980	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs560389	0.87[CEU][hapmap]
rs563113	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs569593	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs570368	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6603962	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6603971	0.80[ASN][1000 genomes]
rs6603973	0.86[EUR][1000 genomes]
rs6604082	1.00[JPT][hapmap]
rs6604088	0.80[ASN][1000 genomes]
rs6604090	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6661384	0.80[ASN][1000 genomes]
rs6662379	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662920	0.84[EUR][1000 genomes]
rs6663278	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6663905	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668803	1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs66758257	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6702267	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs72720457	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs733012	0.80[ASN][1000 genomes]
rs745793	0.80[ASN][1000 genomes]
rs7517541	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7518974	0.80[ASN][1000 genomes]
rs7520275	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7522081	0.80[EUR][1000 genomes]
rs7524120	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539757	0.80[ASN][1000 genomes]
rs7543947	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7550680	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439911	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9943178	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	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
6	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS 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
8	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

No data

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	chr1:92784400-92808200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:92789800-92812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:92790000-92815200	Weak transcription	Psoas Muscle	Psoas
7	chr1:92792400-92817400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:92792400-92823600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:92792600-92807600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:92792600-92807800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:92792600-92812400	Weak transcription	Right Ventricle	heart
12	chr1:92792600-92815000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:92792600-92846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:92792800-92850800	Weak transcription	Fetal Heart	heart
15	chr1:92793600-92817200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:92793600-92823400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:92793800-92806600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:92793800-92811800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:92793800-92830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:92794000-92823000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:92794800-92807600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:92795000-92817600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:92795000-92823000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:92795200-92806400	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:92795200-92806600	Weak transcription	Fetal Stomach	stomach
26	chr1:92795200-92807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:92795200-92815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:92795200-92817000	Weak transcription	Esophagus	oesophagus
29	chr1:92795200-92817000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:92795200-92823400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:92795200-92825000	Weak transcription	Aorta	Aorta
32	chr1:92795200-92825000	Weak transcription	Lung	lung
33	chr1:92795200-92830400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:92795200-92846600	Weak transcription	Gastric	stomach
35	chr1:92795200-92850200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:92795200-92851400	Weak transcription	Spleen	Spleen
37	chr1:92795400-92807000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:92795400-92825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:92795600-92814400	Weak transcription	A549	lung
40	chr1:92795600-92825200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:92795600-92826400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:92795600-92831200	Weak transcription	NHLF	lung
43	chr1:92795800-92805800	Weak transcription	Fetal Lung	lung
44	chr1:92795800-92806600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:92795800-92806600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:92795800-92807800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:92795800-92807800	Weak transcription	Thymus	Thymus
48	chr1:92795800-92808000	Weak transcription	Ovary	ovary
49	chr1:92795800-92810800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:92795800-92817600	Weak transcription	Brain Angular Gyrus	brain

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