Variant report

Variant	rs7540216
Chromosome Location	chr1:185175016-185175017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10489582	1.00[EUR][1000 genomes]
rs10494582	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs11804954	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12024255	1.00[EUR][1000 genomes]
rs12026308	1.00[EUR][1000 genomes]
rs12033761	1.00[EUR][1000 genomes]
rs12037199	1.00[EUR][1000 genomes]
rs12038977	1.00[EUR][1000 genomes]
rs12041641	1.00[EUR][1000 genomes]
rs12045533	1.00[EUR][1000 genomes]
rs12240005	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12240119	0.81[AMR][1000 genomes]
rs16823734	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs16823739	1.00[EUR][1000 genomes]
rs16823862	1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823869	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs16823875	1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823884	1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823891	0.89[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2025228	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144664	1.00[EUR][1000 genomes]
rs3766713	1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3766716	1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3895195	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs41377350	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57266144	1.00[EUR][1000 genomes]
rs57927210	1.00[EUR][1000 genomes]
rs57960155	1.00[EUR][1000 genomes]
rs58031282	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58292874	0.90[AMR][1000 genomes]
rs58685423	1.00[EUR][1000 genomes]
rs59035619	1.00[EUR][1000 genomes]
rs59227355	1.00[EUR][1000 genomes]
rs59611551	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59818790	1.00[EUR][1000 genomes]
rs60064915	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379702	1.00[EUR][1000 genomes]
rs61537994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61573899	1.00[EUR][1000 genomes]
rs6672580	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs6674689	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs6679946	0.86[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687946	1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs6695308	0.84[ASW][hapmap];0.85[YRI][hapmap]
rs6698620	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515757	0.81[AMR][1000 genomes]
rs7516303	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555243	1.00[EUR][1000 genomes]
rs953701	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs953702	0.90[AMR][1000 genomes];1.00[EUR][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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
3	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
4	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:185128400-185201800	Weak transcription	Gastric	stomach
6	chr1:185134600-185193200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:185137200-185177200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:185137200-185191400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:185137400-185177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:185137400-185191200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:185137400-185191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:185138000-185182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:185138000-185186200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:185138000-185204000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:185139600-185177400	Weak transcription	Fetal Kidney	kidney
16	chr1:185139800-185191400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:185140000-185190800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:185140000-185191600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:185144800-185181200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:185145000-185182400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:185145200-185191400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:185148400-185193400	Weak transcription	Fetal Thymus	thymus
23	chr1:185151000-185193200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:185152200-185200800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:185153200-185191600	Weak transcription	Aorta	Aorta
26	chr1:185154400-185191600	Weak transcription	Ovary	ovary
27	chr1:185158600-185176400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:185159600-185177600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:185160000-185192600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:185160600-185191600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:185160800-185192000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:185161800-185191400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:185162000-185190800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:185163600-185190600	Weak transcription	Placenta	Placenta
35	chr1:185167600-185177400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:185167600-185177600	Weak transcription	Liver	Liver
37	chr1:185167800-185182200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:185168000-185201800	Weak transcription	Primary T cells from cord blood	blood
39	chr1:185168200-185191400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:185168400-185192200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:185169400-185177800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:185170000-185179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:185170400-185192000	Weak transcription	Fetal Intestine Large	intestine
44	chr1:185170800-185191600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:185170800-185191600	Weak transcription	Fetal Intestine Small	intestine
46	chr1:185170800-185191600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:185170800-185192600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:185170800-185199800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:185170800-185218200	Weak transcription	Pancreas	Pancrea
50	chr1:185171000-185176400	Weak transcription	Lung	lung

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