Variant report

Variant	rs17713646
Chromosome Location	chr22:30375965-30375966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30369409..30372830-chr22:30374993..30377919,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10222281	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483156	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11090591	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11090592	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11703553	0.81[EUR][1000 genomes]
rs11703815	0.81[EUR][1000 genomes]
rs11704206	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11704885	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11705207	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705418	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12159277	0.80[CHB][hapmap]
rs12165769	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12166755	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12166998	0.95[ASN][1000 genomes]
rs12169823	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330007	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12330076	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627856	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12627866	0.80[CHB][hapmap]
rs12627944	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12628395	0.83[ASN][1000 genomes]
rs12628545	0.80[CHB][hapmap]
rs16988049	0.80[CHB][hapmap]
rs17644868	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17644886	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17647135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17711461	0.80[CHB][hapmap]
rs17711508	0.80[CHB][hapmap]
rs2240364	0.80[CHB][hapmap]
rs2240365	0.80[CHB][hapmap]
rs2240366	0.80[CHB][hapmap]
rs28520101	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635872	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34647160	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747148	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3788418	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3788425	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285800	0.80[CHB][hapmap]
rs737905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737906	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737907	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739615	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs740116	0.80[CHB][hapmap]
rs916782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9614123	1.00[JPT][hapmap]
rs9620928	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9620929	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9620935	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620936	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620944	0.87[ASN][1000 genomes]
rs9625883	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625886	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625887	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625889	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625894	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625895	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625896	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625899	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625910	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30340800-30376000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:30344400-30376000	Weak transcription	HSMMtube	muscle
3	chr22:30345400-30379000	Weak transcription	Esophagus	oesophagus
4	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
6	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr22:30351200-30387400	Weak transcription	Ovary	ovary
8	chr22:30352800-30388600	Weak transcription	HepG2	liver
9	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
10	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
11	chr22:30356200-30376600	Weak transcription	Fetal Kidney	kidney
12	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr22:30366600-30390800	Weak transcription	Gastric	stomach
17	chr22:30366800-30376000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:30368400-30382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:30368400-30387400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr22:30369400-30382600	Weak transcription	Brain Anterior Caudate	brain
23	chr22:30369400-30388400	Weak transcription	NH-A	brain
24	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
25	chr22:30370200-30388400	Weak transcription	NHLF	lung
26	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
27	chr22:30370800-30379400	Weak transcription	HSMM	muscle
28	chr22:30370800-30387400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:30370800-30390000	Weak transcription	Stomach Mucosa	stomach
30	chr22:30371000-30383200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr22:30371200-30382000	Weak transcription	Brain Substantia Nigra	brain
32	chr22:30371800-30385800	Weak transcription	Lung	lung
33	chr22:30371800-30386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:30372600-30377800	Strong transcription	Fetal Muscle Leg	muscle
35	chr22:30373400-30383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr22:30373400-30388600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:30373600-30377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr22:30373600-30377800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr22:30373600-30383400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr22:30373600-30383600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:30373600-30388600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr22:30373800-30377600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr22:30374000-30376400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:30374000-30376800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr22:30374000-30377400	Strong transcription	Placenta	Placenta
47	chr22:30374000-30377600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:30374000-30380000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr22:30374200-30377000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr22:30374200-30377000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links