Variant report

Variant	rs17117974
Chromosome Location	chr12:56165949-56165950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56164086..56166106-chr12:56181823..56184194,3	K562	blood:
2	chr12:56160238..56162855-chr12:56164043..56166481,2	MCF-7	breast:
3	chr12:56165177..56167072-chr12:56175490..56177284,2	MCF-7	breast:
4	chr12:56159003..56161708-chr12:56163699..56166884,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10082864	0.85[ASN][1000 genomes]
rs10083186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10161417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11171667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11171670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171671	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171681	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11829536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11834264	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12304296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12304507	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12320756	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291267	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs3759101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7297523	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7299222	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7972345	0.84[ASN][1000 genomes]
rs868051	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9739244	0.88[ASN][1000 genomes]

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	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56139400-56174600	Weak transcription	Stomach Mucosa	stomach
2	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56143800-56170000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:56144800-56198600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr12:56145200-56199400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:56146600-56166200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:56150000-56167000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:56152000-56173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:56152600-56171400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:56152600-56179600	Weak transcription	Pancreas	Pancrea
13	chr12:56152800-56166200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:56153000-56174600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:56153000-56176400	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:56153000-56182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:56153200-56171600	Weak transcription	Esophagus	oesophagus
19	chr12:56153400-56175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:56153800-56170600	Weak transcription	Ovary	ovary
21	chr12:56154400-56178400	Weak transcription	Fetal Brain Male	brain
22	chr12:56154400-56180600	Weak transcription	Right Ventricle	heart
23	chr12:56155800-56174200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:56156800-56166000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:56157200-56166800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:56159000-56166400	Strong transcription	Fetal Intestine Large	intestine
27	chr12:56159000-56167000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:56159400-56167400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:56159400-56168200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:56160000-56169800	Weak transcription	Gastric	stomach
31	chr12:56160000-56170400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:56160000-56175600	Weak transcription	Spleen	Spleen
33	chr12:56160000-56179600	Weak transcription	Aorta	Aorta
34	chr12:56160000-56197600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:56160200-56180000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:56160200-56184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:56160400-56174800	Weak transcription	NHLF	lung
38	chr12:56160400-56209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:56160800-56168200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:56160800-56174800	Weak transcription	Lung	lung
41	chr12:56161000-56174800	Weak transcription	Brain Germinal Matrix	brain
42	chr12:56162200-56183200	Strong transcription	Primary T cells from cord blood	blood
43	chr12:56162400-56167400	Strong transcription	Liver	Liver
44	chr12:56162400-56173400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:56162600-56166200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:56162800-56166600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:56162800-56167600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:56162800-56168200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:56163000-56166000	Strong transcription	Hela-S3	cervix
50	chr12:56163000-56166000	Strong transcription	HUVEC	blood vessel

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