Variant report

Variant	rs2508443
Chromosome Location	chr11:57377992-57377993
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10792101	0.82[CHB][hapmap]
rs10792106	0.82[CHB][hapmap]
rs1115172	0.82[CHB][hapmap]
rs1557522	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081362	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2244169	0.89[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454660	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508441	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2509897	0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2511989	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2511990	0.89[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2511991	0.85[ASN][1000 genomes]
rs2511993	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2511994	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2511996	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2649664	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2729376	0.89[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2848627	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2926664	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938869	0.82[CHB][hapmap]
rs4938871	0.82[CHB][hapmap]
rs4939151	0.82[CHB][hapmap]
rs4939152	0.82[CHB][hapmap]
rs7123582	0.82[CHB][hapmap]
rs7124330	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2508443	YPEL4	cis	multi-tissue	Pritchard
rs2508443	TIMM10	cis	parietal	SCAN
rs2508443	CD5	cis	parietal	SCAN
rs2508443	YPEL4	cis	lymphoblastoid	seeQTL
rs2508443	TIMM10	cis	multi-tissue	Pritchard
rs2508443	TNKS1BP1	cis	parietal	SCAN
rs2508443	TIMM10	cis	Esophagus Mucosa	GTEx
rs2508443	OR8J1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57366200-57379000	Weak transcription	Gastric	stomach
2	chr11:57366400-57381800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:57366400-57385800	Weak transcription	Esophagus	oesophagus
4	chr11:57366600-57378800	Weak transcription	Colonic Mucosa	Colon
5	chr11:57366600-57382600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:57366600-57384400	Weak transcription	Pancreas	Pancrea
7	chr11:57366800-57380800	Weak transcription	Brain Anterior Caudate	brain
8	chr11:57366800-57381600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:57366800-57381600	Weak transcription	Osteobl	bone
10	chr11:57366800-57386600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:57366800-57388800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:57367000-57387400	Weak transcription	NHDF-Ad	bronchial
13	chr11:57367200-57378800	Weak transcription	Right Ventricle	heart
14	chr11:57367200-57379200	Weak transcription	Fetal Intestine Large	intestine
15	chr11:57367200-57380600	Weak transcription	Fetal Brain Male	brain
16	chr11:57367200-57380600	Weak transcription	Fetal Kidney	kidney
17	chr11:57367400-57381600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:57369000-57385200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:57369800-57383400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:57369800-57383400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57370000-57379000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:57370000-57385200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:57372000-57379200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:57372200-57379000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:57372200-57384600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:57372600-57384400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:57372800-57382600	Weak transcription	Fetal Thymus	thymus
28	chr11:57372800-57383200	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:57372800-57386600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:57373000-57383000	Strong transcription	Ovary	ovary
31	chr11:57373000-57383200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:57373200-57384400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:57373200-57384400	Strong transcription	Fetal Lung	lung
34	chr11:57373800-57379000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:57373800-57380600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:57373800-57383400	Weak transcription	NHLF	lung
37	chr11:57373800-57391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:57374000-57379000	Weak transcription	Spleen	Spleen
39	chr11:57374000-57380800	Weak transcription	Small Intestine	intestine
40	chr11:57374000-57386000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:57374200-57378800	Weak transcription	Brain Germinal Matrix	brain
42	chr11:57374400-57384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:57374600-57380600	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:57374600-57381200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:57374800-57378800	Weak transcription	Left Ventricle	heart
46	chr11:57375000-57378200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:57375000-57379000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:57375000-57379000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:57375000-57380600	Weak transcription	Fetal Brain Female	brain
50	chr11:57375000-57381000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links