Variant report

Variant	rs538386
Chromosome Location	chr6:149691602-149691603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149691320..149693840-chr6:149697416..149698951,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs17086451	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2143076	0.87[JPT][hapmap]
rs2341783	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744431	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2744433	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2744434	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789487	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789488	0.87[JPT][hapmap]
rs2789489	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789490	0.81[CEU][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734296	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360154	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472620	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs472810	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478531	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs478767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480526	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs480778	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs481769	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897117	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs490529	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504985	0.87[JPT][hapmap]
rs506268	0.82[JPT][hapmap]
rs511105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513923	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs514839	0.87[JPT][hapmap]
rs515133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518879	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521845	0.87[JPT][hapmap]
rs522646	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532008	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533026	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536203	0.87[JPT][hapmap]
rs537354	0.87[JPT][hapmap]
rs540538	0.87[JPT][hapmap]
rs554926	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559052	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559204	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560051	0.87[JPT][hapmap]
rs562428	0.87[JPT][hapmap]
rs564405	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577001	0.87[JPT][hapmap]
rs579789	0.87[JPT][hapmap]
rs588028	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60006373	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630642	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs638407	0.87[JPT][hapmap]
rs641068	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652514	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652807	0.87[JPT][hapmap]
rs652921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570965	0.87[JPT][hapmap]
rs663625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674919	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs681919	0.87[EUR][1000 genomes]
rs909793	0.87[JPT][hapmap]
rs92605	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285519	0.87[JPT][hapmap]
rs9322178	0.87[JPT][hapmap]
rs9373589	0.87[JPT][hapmap]
rs9373591	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377216	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377217	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9377218	0.92[JPT][hapmap]
rs9390676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390677	0.87[JPT][hapmap]
rs9399686	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404032	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404035	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404037	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
2	chr6:149658000-149695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:149658800-149692400	Weak transcription	Fetal Kidney	kidney
4	chr6:149660400-149699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:149662200-149694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:149664000-149694400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:149674600-149691800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:149674600-149699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:149674600-149699200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:149674600-149699200	Weak transcription	Fetal Intestine Large	intestine
11	chr6:149677400-149692400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:149677800-149699200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:149680000-149692400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:149680000-149699200	Weak transcription	Fetal Brain Male	brain
15	chr6:149681000-149694800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:149681200-149699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:149681800-149695000	Weak transcription	Adipose Nuclei	Adipose
18	chr6:149681800-149699200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:149682600-149699200	Weak transcription	Esophagus	oesophagus
20	chr6:149682600-149699200	Weak transcription	Spleen	Spleen
21	chr6:149682600-149709200	Weak transcription	Psoas Muscle	Psoas
22	chr6:149682800-149692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:149682800-149699200	Weak transcription	Lung	lung
24	chr6:149683400-149698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:149683600-149692400	Weak transcription	NH-A	brain
26	chr6:149683600-149699400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:149684400-149698800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:149684600-149699200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:149685000-149694000	Weak transcription	NHEK	skin
30	chr6:149685200-149694800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:149685200-149699200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:149685200-149699400	Weak transcription	HMEC	breast
33	chr6:149685400-149692000	Weak transcription	Small Intestine	intestine
34	chr6:149685400-149692400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:149685600-149699200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:149685600-149699200	Weak transcription	Gastric	stomach
37	chr6:149685600-149699400	Weak transcription	Brain Angular Gyrus	brain
38	chr6:149685600-149699400	Weak transcription	Fetal Intestine Small	intestine
39	chr6:149685800-149691800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:149685800-149692000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:149685800-149692000	Weak transcription	Pancreas	Pancrea
42	chr6:149685800-149692400	Weak transcription	Ovary	ovary
43	chr6:149685800-149699200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:149685800-149699200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:149685800-149699200	Weak transcription	Fetal Stomach	stomach
46	chr6:149685800-149699200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:149685800-149699600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:149686000-149692400	Weak transcription	HepG2	liver
49	chr6:149686000-149699200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:149686000-149709000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links