Variant report

Variant	rs16844866
Chromosome Location	chr2:161063407-161063408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:161023086..161025221-chr2:161061851..161065492,3	MCF-7	breast:
2	chr2:161011891..161014884-chr2:161060421..161064713,4	MCF-7	breast:
3	chr17:56736235..56738375-chr2:161062578..161064642,2	MCF-7	breast:
4	chr2:161011380..161016239-chr2:161062030..161067547,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10497213	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10929965	0.90[JPT][hapmap]
rs13001911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16844848	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16844863	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844875	0.85[JPT][hapmap]
rs17216980	0.95[JPT][hapmap]
rs17218566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17241282	0.81[JPT][hapmap]
rs17341301	0.86[JPT][hapmap]
rs17830904	0.81[JPT][hapmap]
rs17831161	0.91[JPT][hapmap]
rs17831191	0.91[JPT][hapmap]
rs17831251	0.90[JPT][hapmap]
rs1870102	0.93[ASN][1000 genomes]
rs1870104	0.94[ASN][1000 genomes]
rs2124969	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2175416	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2198918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2305818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2305819	0.86[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs3749117	0.81[JPT][hapmap]
rs3749119	0.91[JPT][hapmap]
rs3792192	0.81[JPT][hapmap]
rs4292050	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4664308	0.90[JPT][hapmap]
rs4664317	0.83[ASN][1000 genomes]
rs4665138	0.81[JPT][hapmap]
rs4665140	0.82[JPT][hapmap]
rs4665141	0.83[JPT][hapmap]
rs4665147	0.90[JPT][hapmap]
rs4665161	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55959207	0.90[ASN][1000 genomes]
rs57993273	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59019419	0.99[ASN][1000 genomes]
rs59541669	0.91[ASN][1000 genomes]
rs60608133	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60801510	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60908067	0.80[ASN][1000 genomes]
rs61330151	0.92[ASN][1000 genomes]
rs62175395	0.95[ASN][1000 genomes]
rs6705574	0.86[JPT][hapmap]
rs6707458	0.90[JPT][hapmap]
rs6719686	0.91[JPT][hapmap]
rs6722275	0.81[JPT][hapmap]
rs6731260	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6732107	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739867	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6759836	0.91[JPT][hapmap]
rs72623108	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72623109	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72623111	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733810	0.92[ASN][1000 genomes]
rs7589820	0.87[ASN][1000 genomes]
rs7595859	0.95[ASN][1000 genomes]
rs877200	0.90[JPT][hapmap]
rs925410	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:161051800-161064600	Weak transcription	Lung	lung
2	chr2:161052200-161064600	Weak transcription	Gastric	stomach
3	chr2:161053200-161064600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:161057600-161064200	Weak transcription	Fetal Intestine Large	intestine
5	chr2:161059200-161065200	Weak transcription	Psoas Muscle	Psoas
6	chr2:161059600-161068000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:161060000-161066200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:161060200-161066800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:161060400-161064200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:161060600-161064600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:161061200-161064400	Enhancers	NH-A	brain
12	chr2:161061200-161067800	Enhancers	NHDF-Ad	bronchial
13	chr2:161061400-161066200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:161061400-161068600	Enhancers	Stomach Mucosa	stomach
15	chr2:161061800-161064800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:161061800-161064800	Weak transcription	Esophagus	oesophagus
17	chr2:161062000-161063800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:161062000-161064000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:161062000-161064200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:161062000-161064600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:161062200-161064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:161062200-161070000	Weak transcription	Aorta	Aorta
23	chr2:161062400-161063600	Weak transcription	Placenta	Placenta
24	chr2:161062400-161064200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:161062400-161064600	Enhancers	Small Intestine	intestine
26	chr2:161062600-161063600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:161062600-161063800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:161062600-161064000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:161062600-161064200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:161062600-161064200	Enhancers	Hela-S3	cervix
31	chr2:161062600-161064400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:161062600-161064800	Weak transcription	Spleen	Spleen
33	chr2:161062600-161066200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:161062800-161063800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:161062800-161063800	Weak transcription	Osteobl	bone
36	chr2:161062800-161066000	Enhancers	GM12878-XiMat	blood
37	chr2:161062800-161069200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:161062800-161069200	Enhancers	HUVEC	blood vessel
39	chr2:161063000-161064000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:161063000-161064000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:161063000-161064000	Weak transcription	NHLF	lung
42	chr2:161063000-161064200	Weak transcription	Colonic Mucosa	Colon
43	chr2:161063000-161066600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:161063000-161067800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:161063200-161063600	ZNF genes & repeats	A549	lung
46	chr2:161063200-161064000	Enhancers	HSMMtube	muscle
47	chr2:161063200-161064200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:161063200-161064200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:161063200-161064200	Weak transcription	Dnd41	blood
50	chr2:161063200-161064400	Enhancers	HMEC	breast

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