Variant report

Variant	rs5743003
Chromosome Location	chr2:190667069-190667070
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190666669..190670194-chr2:190675101..190678586,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1046196	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233267	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233270	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233273	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233274	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233286	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13404927	0.82[EUR][1000 genomes]
rs2544054	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5742924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742955	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742965	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742976	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742991	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742993	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742994	0.81[EUR][1000 genomes]
rs5742997	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743024	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs5743028	0.91[AFR][1000 genomes]
rs5743048	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743067	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743090	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743102	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743130	0.82[EUR][1000 genomes]
rs58147864	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60386871	0.82[EUR][1000 genomes]
rs6750293	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73042330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73054335	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735558	0.82[EUR][1000 genomes]
rs7579156	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3080	chr2:190661654-190706515	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3369169	chr2:190667021-190667130	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
2	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
3	chr2:190649800-190713400	Weak transcription	Gastric	stomach
4	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:190650200-190668200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:190650200-190669200	Weak transcription	Right Ventricle	heart
7	chr2:190650200-190673000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:190650200-190673200	Weak transcription	Small Intestine	intestine
9	chr2:190650400-190667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:190650400-190670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:190650400-190675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
13	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
14	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:190650600-190668200	Weak transcription	Fetal Brain Female	brain
17	chr2:190650600-190683200	Weak transcription	Fetal Brain Male	brain
18	chr2:190650600-190688800	Weak transcription	Fetal Heart	heart
19	chr2:190650600-190693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
21	chr2:190650800-190675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:190651000-190673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:190651000-190673400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:190651200-190673800	Weak transcription	Brain Germinal Matrix	brain
25	chr2:190653400-190673000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:190655000-190671800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:190656200-190670800	Strong transcription	HepG2	liver
28	chr2:190656200-190673000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:190656200-190677800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:190656800-190685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:190657600-190669400	Strong transcription	Fetal Thymus	thymus
33	chr2:190658000-190671400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:190659000-190685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:190659200-190668800	Weak transcription	Ovary	ovary
37	chr2:190659200-190681200	Weak transcription	Spleen	Spleen
38	chr2:190659800-190686800	Weak transcription	Fetal Stomach	stomach
39	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:190661000-190674400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:190661200-190673000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:190661400-190670400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:190661800-190669000	Weak transcription	Placenta	Placenta
45	chr2:190662600-190674600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:190662600-190683000	Weak transcription	Adipose Nuclei	Adipose
47	chr2:190662600-190686800	Weak transcription	Left Ventricle	heart
48	chr2:190662800-190667200	Weak transcription	Primary B cells from cord blood	blood
49	chr2:190662800-190667400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:190662800-190674600	Weak transcription	Duodenum Mucosa	Duodenum

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