Variant report

Variant	rs62175380
Chromosome Location	chr2:161001376-161001377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:161000112..161002842-chr2:161027169..161029887,2	MCF-7	breast:
2	chr2:161000991..161002542-chr2:161026874..161029211,2	MCF-7	breast:
3	chr2:160992962..160995573-chr2:161000331..161001986,2	K562	blood:
4	chr2:160992962..160997280-chr2:160998915..161002711,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10497212	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12478287	0.88[ASN][1000 genomes]
rs16844742	0.85[ASN][1000 genomes]
rs16844790	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16844802	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17284082	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28867432	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111395	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4076843	0.88[ASN][1000 genomes]
rs4595921	0.88[ASN][1000 genomes]
rs4665154	0.88[ASN][1000 genomes]
rs4665156	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58716738	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60454853	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60915384	0.88[ASN][1000 genomes]
rs62175383	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62175385	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62175389	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62175390	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62177892	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72967898	0.88[ASN][1000 genomes]
rs72969807	0.86[ASN][1000 genomes]
rs72969809	0.88[ASN][1000 genomes]
rs72975471	0.88[ASN][1000 genomes]
rs72975474	0.88[ASN][1000 genomes]
rs72977408	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72979930	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557804	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573469	0.88[ASN][1000 genomes]
rs7581712	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv528083	chr2:160998792-161015066	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160959200-161004200	Weak transcription	Gastric	stomach
2	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
3	chr2:160983200-161005200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:160990000-161005000	Weak transcription	Colonic Mucosa	Colon
5	chr2:160993200-161002200	Weak transcription	Lung	lung
6	chr2:160994400-161002000	Weak transcription	Esophagus	oesophagus
7	chr2:160994400-161002000	Weak transcription	Fetal Intestine Large	intestine
8	chr2:160994400-161004200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:160994400-161014800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:160994400-161037400	Weak transcription	Pancreas	Pancrea
11	chr2:160994600-161038000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:160994800-161002000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:160997200-161002000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:160997200-161014600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:160997200-161021800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:160999400-161004800	Weak transcription	A549	lung
17	chr2:160999400-161012800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:160999400-161022600	Weak transcription	Stomach Mucosa	stomach
19	chr2:160999800-161002600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:160999800-161005600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:161000400-161004800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:161000600-161001400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:161000600-161002600	Enhancers	Dnd41	blood
24	chr2:161000600-161005600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:161000800-161001800	Strong transcription	HSMM	muscle
26	chr2:161000800-161002600	Strong transcription	NHEK	skin
27	chr2:161000800-161003600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:161001000-161002400	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:161001000-161004000	Strong transcription	HMEC	breast
30	chr2:161001200-161001400	Enhancers	Fetal Kidney	kidney
31	chr2:161001200-161001600	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links