Variant report

Variant	rs2850972
Chromosome Location	chr4:102186151-102186152
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	chr4:102161014..102163978-chr4:102184167..102186813,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1157038	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1395474	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1472825	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2135608	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2135609	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2135612	0.88[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659516	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659517	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659518	0.90[EUR][1000 genomes]
rs2659519	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659520	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659521	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659522	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659523	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659525	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659527	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659529	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659530	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2659531	0.87[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850347	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2850365	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2850373	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2850951	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2850989	0.87[CEU][hapmap]
rs2850996	0.83[EUR][1000 genomes]
rs2850998	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2850999	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851001	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851002	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851003	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851009	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4478191	1.00[ASW][hapmap]
rs67445056	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs970071	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
2	chr4:102179000-102186800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:102180600-102186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:102180600-102186200	Weak transcription	Pancreas	Pancrea
5	chr4:102180600-102191000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:102180600-102192400	Weak transcription	Ovary	ovary
7	chr4:102180600-102197000	Weak transcription	Left Ventricle	heart
8	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:102180800-102186200	Weak transcription	Gastric	stomach
10	chr4:102181200-102186600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:102181200-102186800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:102182600-102189800	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:102182600-102192600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:102183000-102187600	Enhancers	Primary B cells from cord blood	blood
15	chr4:102183400-102186800	Enhancers	Primary B cells from peripheral blood	blood
16	chr4:102183600-102186800	Enhancers	Stomach Mucosa	stomach
17	chr4:102183800-102188200	Enhancers	HepG2	liver
18	chr4:102184000-102203200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:102184200-102194600	Weak transcription	Psoas Muscle	Psoas
20	chr4:102184400-102199600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:102184600-102188000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:102184600-102199400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:102185000-102187000	Enhancers	HUVEC	blood vessel
24	chr4:102185200-102187200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:102185200-102192600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:102185400-102186200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:102185400-102193600	Weak transcription	Brain Anterior Caudate	brain
28	chr4:102185600-102186200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:102185600-102186600	Enhancers	Small Intestine	intestine
30	chr4:102185800-102186200	Flanking Active TSS	A549	lung
31	chr4:102185800-102186400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:102185800-102186600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:102185800-102187200	Enhancers	Liver	Liver
34	chr4:102185800-102187400	Enhancers	HMEC	breast
35	chr4:102186000-102186200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr4:102186000-102186200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:102186000-102186800	Enhancers	NHEK	skin
38	chr4:102186000-102187000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:102186000-102187400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:102186000-102188400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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