Variant report

Variant	rs72892441
Chromosome Location	chr6:80907886-80907887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:80907847-80907975	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
BCKDHB	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1040593	0.83[ASN][1000 genomes]
rs1179571	1.00[ASN][1000 genomes]
rs12525046	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526876	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527244	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528770	0.82[EUR][1000 genomes]
rs12529191	0.82[EUR][1000 genomes]
rs12530290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891532	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891545	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706829	1.00[ASN][1000 genomes]
rs4706830	1.00[ASN][1000 genomes]
rs55755254	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57913486	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57985210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584372	1.00[ASN][1000 genomes]
rs585506	1.00[ASN][1000 genomes]
rs587999	1.00[ASN][1000 genomes]
rs588009	1.00[ASN][1000 genomes]
rs590686	1.00[ASN][1000 genomes]
rs59552964	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs598234	1.00[ASN][1000 genomes]
rs59973779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610946	1.00[ASN][1000 genomes]
rs612208	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs613577	1.00[ASN][1000 genomes]
rs623085	1.00[ASN][1000 genomes]
rs631367	1.00[ASN][1000 genomes]
rs634499	1.00[ASN][1000 genomes]
rs636499	1.00[ASN][1000 genomes]
rs638921	1.00[ASN][1000 genomes]
rs640568	1.00[ASN][1000 genomes]
rs641229	1.00[ASN][1000 genomes]
rs642943	1.00[ASN][1000 genomes]
rs644666	1.00[ASN][1000 genomes]
rs6454149	1.00[ASN][1000 genomes]
rs646369	1.00[ASN][1000 genomes]
rs649148	1.00[ASN][1000 genomes]
rs651065	1.00[ASN][1000 genomes]
rs66518170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66560352	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66606872	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs669420	1.00[ASN][1000 genomes]
rs670119	1.00[ASN][1000 genomes]
rs670390	1.00[ASN][1000 genomes]
rs67379633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67456645	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67597629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677134	1.00[ASN][1000 genomes]
rs67851250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67988458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688442	1.00[ASN][1000 genomes]
rs6906403	1.00[ASN][1000 genomes]
rs6908084	1.00[ASN][1000 genomes]
rs6920430	0.83[ASN][1000 genomes]
rs6924011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723308	1.00[ASN][1000 genomes]
rs72892417	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892426	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906886	0.82[EUR][1000 genomes]
rs72906894	0.82[EUR][1000 genomes]
rs72908809	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72908830	0.81[EUR][1000 genomes]
rs72908854	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755034	0.82[EUR][1000 genomes]
rs7757610	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771047	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7771726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772483	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806781	1.00[ASN][1000 genomes]
rs806839	1.00[ASN][1000 genomes]
rs806844	0.83[ASN][1000 genomes]
rs806846	0.83[ASN][1000 genomes]
rs806850	0.83[ASN][1000 genomes]
rs811567	1.00[ASN][1000 genomes]
rs932463	1.00[ASN][1000 genomes]
rs9443739	1.00[ASN][1000 genomes]
rs9688524	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80842200-80914200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:80878000-80921000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:80878600-80916000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:80878800-80914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:80880600-80914200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:80882400-80935400	Weak transcription	Dnd41	blood
7	chr6:80883800-80913200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:80885800-80919000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:80891600-80931200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:80892200-80913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:80896200-80921000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:80896400-80927400	Weak transcription	Aorta	Aorta
13	chr6:80896400-80943800	Weak transcription	Right Ventricle	heart
14	chr6:80897800-80918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:80904200-80921800	Weak transcription	Fetal Thymus	thymus
16	chr6:80904400-80913000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:80904400-80916200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:80905000-80919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:80905600-80923800	Weak transcription	Small Intestine	intestine
20	chr6:80906400-80908000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:80906600-80908000	Enhancers	Liver	Liver
22	chr6:80906600-80908000	Enhancers	Fetal Brain Female	brain
23	chr6:80906800-80908200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:80906800-80908800	Enhancers	Brain Germinal Matrix	brain
25	chr6:80907000-80908000	Enhancers	Brain Hippocampus Middle	brain
26	chr6:80907200-80908000	Enhancers	Brain Angular Gyrus	brain
27	chr6:80907200-80908000	Enhancers	Brain Anterior Caudate	brain
28	chr6:80907200-80908000	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:80907200-80908000	Enhancers	Colon Smooth Muscle	Colon
30	chr6:80907200-80908000	Enhancers	Fetal Muscle Leg	muscle
31	chr6:80907200-80908000	Enhancers	Left Ventricle	heart
32	chr6:80907200-80908000	Enhancers	HSMMtube	muscle
33	chr6:80907200-80909000	Enhancers	Psoas Muscle	Psoas
34	chr6:80907400-80908000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:80907400-80908000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:80907400-80908000	Enhancers	Fetal Lung	lung
37	chr6:80907400-80912600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:80907400-80919800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:80907400-80920400	Weak transcription	Gastric	stomach
40	chr6:80907600-80908000	Flanking Active TSS	Fetal Heart	heart
41	chr6:80907600-80914000	Weak transcription	Ovary	ovary
42	chr6:80907600-80915000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:80907600-80916800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:80907600-80917000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:80907600-80920400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:80907600-80920400	Weak transcription	NHDF-Ad	bronchial
47	chr6:80907800-80908000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:80907800-80908800	Weak transcription	Right Atrium	heart
49	chr6:80907800-80912800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:80907800-80913200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links