Variant report

Variant	rs2050648
Chromosome Location	chr1:94889414-94889415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94882805..94885755-chr1:94886317..94890931,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117528	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10157506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034363	0.87[EUR][1000 genomes]
rs1041282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165149	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11576665	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11581292	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11582033	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158254	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585880	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12120731	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127355	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130330	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12131298	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12143221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143512	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17410399	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147794	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296382	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2794470	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148042	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148050	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148056	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4536006	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801886	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56353982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61772847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61772851	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61772854	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698950	0.82[EUR][1000 genomes]
rs7555399	0.89[EUR][1000 genomes]
rs841692	0.86[EUR][1000 genomes]
rs841695	0.86[EUR][1000 genomes]
rs927728	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966176	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871097	chr1:94850443-94941890	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94885000-94889800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:94885200-94889800	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr1:94885200-94891000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94885200-94907200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:94885200-94915000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:94885400-94889800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:94885600-94889800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:94885600-94891200	Weak transcription	Adipose Nuclei	Adipose
9	chr1:94885600-94891800	Weak transcription	Fetal Stomach	stomach
10	chr1:94885800-94889600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:94885800-94891000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:94885800-94891000	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:94885800-94891400	Weak transcription	Fetal Lung	lung
14	chr1:94885800-94894000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:94885800-94894000	Weak transcription	Colonic Mucosa	Colon
16	chr1:94886000-94889800	Enhancers	Stomach Mucosa	stomach
17	chr1:94886000-94891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:94886000-94891400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:94886000-94891400	Weak transcription	Fetal Kidney	kidney
20	chr1:94886000-94891600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:94886200-94891400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:94886200-94891400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:94886400-94889600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:94886400-94891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:94886600-94889800	Enhancers	A549	lung
26	chr1:94886800-94891000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:94887000-94889600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:94887200-94889600	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr1:94887400-94890400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:94887400-94894800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:94887600-94890400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:94887800-94889800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:94887800-94891000	Weak transcription	Fetal Intestine Small	intestine
34	chr1:94888000-94889600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:94888000-94890000	Enhancers	Small Intestine	intestine
36	chr1:94888000-94891200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:94888000-94892600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:94888000-94894200	Weak transcription	Right Ventricle	heart
39	chr1:94888000-94895000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:94888000-94895400	Weak transcription	Lung	lung
41	chr1:94888000-94902200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:94888200-94890000	Weak transcription	Left Ventricle	heart
43	chr1:94888200-94890200	Enhancers	Thymus	Thymus
44	chr1:94888200-94891000	Enhancers	Liver	Liver
45	chr1:94888200-94891200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:94888200-94894000	Weak transcription	Gastric	stomach
47	chr1:94888200-94905400	Weak transcription	Right Atrium	heart
48	chr1:94888400-94890400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:94888400-94891400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:94888400-94891400	Weak transcription	Rectal Smooth Muscle	rectum

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