Variant report

Variant	rs6691402
Chromosome Location	chr1:62143569-62143570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62136630..62139811-chr1:62142611..62146521,3	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11207807	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207808	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151756	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151757	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151759	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151762	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151770	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151773	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151775	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1151776	0.91[EUR][1000 genomes]
rs12117475	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124430	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130241	0.87[EUR][1000 genomes]
rs12130439	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134102	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134205	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134428	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137410	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12141280	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12141298	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12144284	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286624	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286625	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286626	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1286628	0.93[EUR][1000 genomes]
rs1286629	0.93[EUR][1000 genomes]
rs1286630	0.93[EUR][1000 genomes]
rs1286634	0.96[EUR][1000 genomes]
rs1611797	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1620169	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1692131	0.93[EUR][1000 genomes]
rs17378384	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051135	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051136	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2799626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4443919	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666057	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6697770	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72672375	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72672390	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674608	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7536565	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538825	0.94[EUR][1000 genomes]
rs7539026	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550631	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62146400	Weak transcription	Gastric	stomach
2	chr1:62120400-62148200	Weak transcription	Aorta	Aorta
3	chr1:62126000-62145800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:62126000-62148800	Weak transcription	Left Ventricle	heart
5	chr1:62126000-62165200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:62131600-62151400	Weak transcription	Lung	lung
7	chr1:62131600-62163800	Weak transcription	Thymus	Thymus
8	chr1:62134800-62164400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:62134800-62164400	Weak transcription	Right Ventricle	heart
10	chr1:62135000-62146000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:62135000-62165000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:62135400-62146200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:62136000-62146000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:62136000-62151200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:62136000-62153400	Weak transcription	NHDF-Ad	bronchial
16	chr1:62136600-62145600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:62136600-62145800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:62136600-62151800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:62136800-62144000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:62136800-62173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:62137000-62146000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:62137000-62146200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:62137200-62145400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:62137400-62144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:62137400-62146000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:62137400-62146200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:62137600-62145600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:62137800-62144200	Weak transcription	Adipose Nuclei	Adipose
29	chr1:62138000-62146200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:62138400-62145800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:62138400-62146200	Weak transcription	Esophagus	oesophagus
32	chr1:62138600-62148000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:62138800-62146200	Weak transcription	Fetal Lung	lung
34	chr1:62138800-62146200	Weak transcription	HMEC	breast
35	chr1:62138800-62189600	Weak transcription	Psoas Muscle	Psoas
36	chr1:62139200-62144200	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:62139800-62145600	Weak transcription	Primary T cells from cord blood	blood
38	chr1:62139800-62146200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:62139800-62146200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:62140000-62189000	Weak transcription	NHLF	lung
41	chr1:62140200-62163800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:62141000-62144200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:62141400-62146000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:62141600-62145600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:62141600-62146200	Weak transcription	GM12878-XiMat	blood
46	chr1:62142000-62144400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:62142000-62146000	Weak transcription	HSMM	muscle
48	chr1:62142200-62143800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:62142200-62146000	Weak transcription	Fetal Thymus	thymus
50	chr1:62142200-62149400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links