Variant report

Variant	rs17051977
Chromosome Location	chr3:52182944-52182945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52028549..52031119-chr3:52180980..52184186,4	MCF-7	breast:
2	chr3:52179622..52181166-chr3:52182583..52184557,2	MCF-7	breast:
3	chr3:52182912..52184820-chr3:52186743..52190018,3	K562	blood:
4	chr3:52015046..52018580-chr3:52182677..52185776,4	K562	blood:
5	chr3:52178543..52180875-chr3:52181836..52184766,2	K562	blood:

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000243989	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs123681	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12386365	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13319566	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164638	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164639	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051957	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171294	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183029	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452586	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28659792	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352146	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352147	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352148	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352149	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352150	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352151	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352153	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664415	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55834589	0.88[EUR][1000 genomes]
rs56281986	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322622	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57335685	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57466127	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59890038	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781635	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72964042	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72964044	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638246	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808787	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876782	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs893056	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9809254	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9809977	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811707	0.84[ASW][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815010	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816434	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817653	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830293	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843299	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847092	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857878	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860982	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865330	0.94[GIH][hapmap];0.88[TSI][hapmap]
rs9868101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:52155200-52187200	Weak transcription	Colonic Mucosa	Colon
3	chr3:52156200-52187600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:52157200-52187600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:52157400-52187200	Weak transcription	Fetal Kidney	kidney
6	chr3:52162400-52184800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:52162800-52187000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52162800-52187200	Weak transcription	NH-A	brain
9	chr3:52163400-52185000	Strong transcription	Thymus	Thymus
10	chr3:52167200-52185200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:52169000-52185000	Strong transcription	Fetal Intestine Small	intestine
12	chr3:52169200-52184200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr3:52169200-52185000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:52169600-52184600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:52169600-52185000	Strong transcription	NHLF	lung
16	chr3:52169600-52186600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52169800-52185200	Strong transcription	Fetal Stomach	stomach
18	chr3:52170800-52187200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:52171200-52187200	Weak transcription	HSMM	muscle
20	chr3:52171200-52187200	Weak transcription	HUVEC	blood vessel
21	chr3:52172400-52185200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:52172400-52187400	Weak transcription	Lung	lung
23	chr3:52173200-52185400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52173600-52185200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:52174400-52185200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52174800-52185200	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr3:52175000-52187600	Weak transcription	Left Ventricle	heart
28	chr3:52175400-52187600	Weak transcription	Psoas Muscle	Psoas
29	chr3:52178400-52183600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:52178400-52184600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52178400-52185000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:52178400-52185200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:52178400-52185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52178400-52185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:52178400-52187400	Weak transcription	Adipose Nuclei	Adipose
36	chr3:52178400-52187400	Weak transcription	Liver	Liver
37	chr3:52178400-52187400	Weak transcription	Brain Angular Gyrus	brain
38	chr3:52178400-52187400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:52178400-52187400	Weak transcription	Fetal Brain Male	brain
40	chr3:52178400-52187400	Weak transcription	Right Ventricle	heart
41	chr3:52178400-52187400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:52178400-52187400	Weak transcription	Small Intestine	intestine
43	chr3:52178400-52187400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:52178400-52187400	Weak transcription	HSMMtube	muscle
45	chr3:52178400-52187600	Weak transcription	Brain Anterior Caudate	brain
46	chr3:52178400-52187600	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:52178400-52187600	Weak transcription	Brain Substantia Nigra	brain
48	chr3:52178400-52187600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:52178600-52184400	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:52178600-52184800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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