Variant report

Variant	rs6688004
Chromosome Location	chr1:120474507-120474508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10127888	0.83[CEU][hapmap]
rs10494235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10923926	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10923929	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10923931	0.83[CEU][hapmap]
rs1493694	0.83[CEU][hapmap]
rs1493695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1493696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493698	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453040	0.83[CEU][hapmap]
rs2453042	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453055	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453058	0.83[CEU][hapmap]
rs2487568	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2493389	0.81[CEU][hapmap]
rs2493391	0.83[CEU][hapmap]
rs2493392	0.83[CEU][hapmap]
rs2493394	0.83[CEU][hapmap]
rs2493398	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2493410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2493411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2493416	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2493419	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2493420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2641316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2641317	0.83[CEU][hapmap]
rs2641338	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793823	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793827	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793829	0.83[CEU][hapmap]
rs2793830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793831	0.83[CEU][hapmap]
rs2934381	0.83[CEU][hapmap]
rs2934387	0.83[CEU][hapmap]
rs327194	0.80[CEU][hapmap]
rs327196	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4659250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5025718	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699780	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515431	0.83[CEU][hapmap]
rs7534585	0.83[CEU][hapmap]
rs7534586	0.83[CEU][hapmap]
rs835573	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835574	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs947273	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120451600-120480000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120452000-120485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:120453000-120476400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:120453000-120483600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:120453200-120475600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:120453400-120476400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:120455400-120475800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr1:120455800-120486800	Strong transcription	Liver	Liver
9	chr1:120456200-120488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:120464200-120476400	Weak transcription	A549	lung
11	chr1:120465200-120479800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:120465400-120476800	Weak transcription	Small Intestine	intestine
13	chr1:120465800-120476800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:120466400-120476600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:120466600-120475600	Weak transcription	Fetal Heart	heart
16	chr1:120466600-120479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:120466600-120479800	Weak transcription	Fetal Brain Female	brain
18	chr1:120466800-120477400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:120468000-120475800	Weak transcription	Fetal Brain Male	brain
20	chr1:120468200-120475600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:120468200-120476200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:120468200-120479000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:120468400-120475600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:120468400-120495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:120468400-120506200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:120468400-120507400	Weak transcription	Right Ventricle	heart
27	chr1:120468600-120475600	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:120468600-120496000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
30	chr1:120468800-120476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:120469200-120476400	Weak transcription	Gastric	stomach
32	chr1:120469400-120475800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:120469400-120476400	Weak transcription	Colonic Mucosa	Colon
34	chr1:120469400-120476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:120469400-120477400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:120469400-120478600	Weak transcription	HepG2	liver
37	chr1:120469600-120476400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:120469600-120485600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:120470000-120474600	Weak transcription	Fetal Intestine Small	intestine
40	chr1:120471000-120475800	Weak transcription	Pancreas	Pancrea
41	chr1:120471200-120475600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:120471200-120475800	Weak transcription	Fetal Kidney	kidney
43	chr1:120471600-120475400	Weak transcription	NH-A	brain
44	chr1:120471800-120475600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:120471800-120475800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:120471800-120476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:120471800-120476400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:120472000-120475000	Weak transcription	Fetal Stomach	stomach
49	chr1:120472000-120475600	Weak transcription	Fetal Lung	lung
50	chr1:120472000-120475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links