Variant report

Variant	rs10025393
Chromosome Location	chr4:143183732-143183733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143181530..143183042-chr4:143183086..143185031,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10004835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107331	0.82[EUR][1000 genomes]
rs13107751	0.85[AMR][1000 genomes]
rs13141901	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13152233	0.80[AMR][1000 genomes]
rs2291338	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34204414	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34564415	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34733226	0.90[AMR][1000 genomes]
rs35107973	0.87[AMR][1000 genomes]
rs35214831	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3775680	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55649528	0.85[AMR][1000 genomes]
rs66600816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997859	0.80[AMR][1000 genomes]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143135400-143184200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:143151000-143185000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:143160600-143185000	Weak transcription	HMEC	breast
4	chr4:143160600-143186400	Weak transcription	HSMM	muscle
5	chr4:143164600-143186000	Weak transcription	HSMMtube	muscle
6	chr4:143171000-143185600	Weak transcription	NHDF-Ad	bronchial
7	chr4:143171000-143185800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:143171000-143186200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:143173200-143184200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:143174400-143185000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:143174600-143186000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:143174600-143190200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:143179200-143186000	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:143179400-143186000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:143179600-143186000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:143179800-143191000	Weak transcription	Colonic Mucosa	Colon
17	chr4:143180200-143185000	Weak transcription	Psoas Muscle	Psoas
18	chr4:143181000-143183800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:143181200-143186400	Weak transcription	NHEK	skin
20	chr4:143181400-143187200	Weak transcription	Right Ventricle	heart
21	chr4:143181400-143191400	Weak transcription	Left Ventricle	heart
22	chr4:143181600-143186000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:143181600-143186000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:143181600-143186200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:143181600-143186200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:143181600-143195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:143181800-143186000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:143181800-143186000	Weak transcription	Dnd41	blood
29	chr4:143181800-143186200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:143182400-143186200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:143182600-143185000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:143182600-143186400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:143182800-143184200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:143182800-143185000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:143183000-143184000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:143183000-143186200	Weak transcription	Osteobl	bone
37	chr4:143183000-143204800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:143183200-143185200	Weak transcription	A549	lung
39	chr4:143183400-143184400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:143183400-143184400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:143183400-143184600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:143183400-143189600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr4:143183600-143184200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:143183600-143189200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links