Variant report

Variant	rs1980228
Chromosome Location	chr8:121054357-121054358
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10090001	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095205	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10095532	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101620	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10101943	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10505376	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs10955948	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1120223	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11780912	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11780985	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12542895	0.83[EUR][1000 genomes]
rs12543907	0.84[EUR][1000 genomes]
rs12545676	0.94[EUR][1000 genomes]
rs12548273	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1519807	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519808	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519812	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1519813	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893478	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs16893517	0.82[EUR][1000 genomes]
rs2292946	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28530768	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875928	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2875931	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4871825	0.88[CEU][hapmap]
rs4871828	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56702755	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57868486	0.82[EUR][1000 genomes]
rs60717250	0.95[EUR][1000 genomes]
rs60754245	0.84[EUR][1000 genomes]
rs6469894	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6469895	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs6469897	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66490854	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66614869	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67872361	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980708	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6993924	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6998730	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004815	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7005228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7007998	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs7013298	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016816	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73315941	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7817016	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7820543	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7821947	0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7822662	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7822927	0.85[EUR][1000 genomes]
rs7824793	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7829101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829116	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7830028	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7833073	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7836087	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7841230	0.85[EUR][1000 genomes]
rs7841621	0.85[EUR][1000 genomes]
rs7843503	0.95[EUR][1000 genomes]
rs955293	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960887	0.96[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1980228	DEPDC6	cis	uninvolved skin	skin_eQTL
rs1980228	DEPDC6	cis	normal skin	skin_eQTL
rs1980228	RP11-760H22.2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
2	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
3	chr8:121032000-121058000	Weak transcription	Pancreas	Pancrea
4	chr8:121036000-121063800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr8:121038400-121061800	Weak transcription	Adipose Nuclei	Adipose
6	chr8:121042000-121063400	Weak transcription	Spleen	Spleen
7	chr8:121045000-121056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:121046200-121065200	Weak transcription	Psoas Muscle	Psoas
9	chr8:121046400-121056600	Weak transcription	Gastric	stomach
10	chr8:121048400-121057800	Weak transcription	Fetal Intestine Small	intestine
11	chr8:121048600-121061800	Weak transcription	Fetal Intestine Large	intestine
12	chr8:121048600-121061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:121048800-121063600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr8:121048800-121063600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:121049200-121062200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:121049200-121072800	Weak transcription	Fetal Lung	lung
17	chr8:121049200-121072800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr8:121049800-121059000	Weak transcription	Fetal Stomach	stomach
19	chr8:121050200-121060200	Weak transcription	Fetal Kidney	kidney
20	chr8:121051200-121054800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:121051600-121056600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:121051600-121056600	Weak transcription	Osteobl	bone
23	chr8:121052800-121054600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr8:121052800-121060000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr8:121053000-121054600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:121053000-121054600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:121053000-121054600	Enhancers	HMEC	breast
28	chr8:121053000-121055000	Enhancers	NHEK	skin
29	chr8:121053000-121059000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:121053200-121054400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:121053400-121054400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr8:121053400-121060400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr8:121053600-121064000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr8:121053600-121067200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:121053600-121072800	Weak transcription	Brain Angular Gyrus	brain
36	chr8:121053600-121072800	Weak transcription	Brain Substantia Nigra	brain
37	chr8:121053600-121072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr8:121053800-121054600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:121053800-121054800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr8:121053800-121055600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr8:121053800-121057000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:121053800-121058000	Weak transcription	Liver	Liver
43	chr8:121053800-121060000	Weak transcription	Ovary	ovary
44	chr8:121053800-121072800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr8:121054000-121054400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr8:121054000-121054400	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:121054000-121055000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:121054000-121058200	Weak transcription	Fetal Muscle Leg	muscle
49	chr8:121054200-121055600	Weak transcription	Colon Smooth Muscle	Colon
50	chr8:121054200-121056800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links