Variant report

Variant	rs12342549
Chromosome Location	chr9:116041061-116041062
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr9:116041029-116041339	HepG2	liver:	n/a	chr9:116041190-116041205
2	POLR2A	chr9:116040914-116041061	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:115512698..115514461-chr9:116038293..116041061,2	MCF-7	breast:
2	chr9:116039888..116041521-chr9:116060320..116062417,2	K562	blood:
3	chr9:116040629..116042415-chr9:116163599..116165929,2	MCF-7	breast:

Variant related genes	Relation type
CDC26	TF binding region
PRPF4	TF binding region
ENSG00000226609	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000148158	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10481674	1.00[JPT][hapmap]
rs10759634	0.80[EUR][1000 genomes]
rs10817464	0.91[ASW][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs10817469	0.86[EUR][1000 genomes]
rs10817471	0.86[EUR][1000 genomes]
rs10817472	0.86[EUR][1000 genomes]
rs10981690	0.80[EUR][1000 genomes]
rs10981695	0.80[EUR][1000 genomes]
rs10981705	0.86[EUR][1000 genomes]
rs10981733	1.00[JPT][hapmap]
rs10981743	1.00[JPT][hapmap]
rs10981745	1.00[JPT][hapmap]
rs10981746	1.00[JPT][hapmap]
rs10981747	1.00[JPT][hapmap]
rs10981748	1.00[JPT][hapmap]
rs11789755	0.95[YRI][hapmap]
rs12006029	1.00[JPT][hapmap]
rs12336832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337552	1.00[JPT][hapmap]
rs12341669	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342197	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343330	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343629	0.95[YRI][hapmap]
rs12348629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349495	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349500	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349614	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12351168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.95[ASN][1000 genomes]
rs12352784	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12352925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543535	1.00[JPT][hapmap]
rs16932583	1.00[JPT][hapmap]
rs16932649	1.00[CHB][hapmap]
rs17764563	1.00[JPT][hapmap]
rs17831256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733164	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437724	1.00[JPT][hapmap]
rs4442214	1.00[JPT][hapmap]
rs4636275	1.00[JPT][hapmap]
rs5012573	1.00[CHB][hapmap]
rs58402825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66509679	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72758255	0.84[EUR][1000 genomes]
rs7858741	0.80[EUR][1000 genomes]
rs7863910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865438	1.00[JPT][hapmap]
rs7875945	1.00[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr9:116038400-116041200	Weak transcription	Gastric	stomach
2	chr9:116038600-116041200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116038600-116042200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:116038600-116050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:116038800-116041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:116038800-116041200	Weak transcription	Aorta	Aorta
7	chr9:116038800-116041200	Weak transcription	Left Ventricle	heart
8	chr9:116038800-116041200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:116038800-116041800	Weak transcription	Fetal Kidney	kidney
10	chr9:116038800-116041800	Weak transcription	Small Intestine	intestine
11	chr9:116038800-116048400	Weak transcription	Stomach Mucosa	stomach
12	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116039000-116041200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:116039000-116041200	Weak transcription	Esophagus	oesophagus
15	chr9:116039000-116041200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:116039000-116041200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:116039000-116041200	Weak transcription	Thymus	Thymus
18	chr9:116039000-116041200	Genic enhancers	Dnd41	blood
19	chr9:116039000-116041800	Weak transcription	Psoas Muscle	Psoas
20	chr9:116039000-116041800	Weak transcription	Spleen	Spleen
21	chr9:116039000-116042000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:116039000-116042000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:116039000-116042000	Weak transcription	Brain Angular Gyrus	brain
24	chr9:116039000-116042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:116039000-116042000	Weak transcription	Right Ventricle	heart
26	chr9:116039000-116042200	Weak transcription	Ovary	ovary
27	chr9:116039000-116042200	Weak transcription	Pancreas	Pancrea
28	chr9:116039000-116042200	Weak transcription	NHDF-Ad	bronchial
29	chr9:116039000-116043400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:116039000-116043400	Weak transcription	Colonic Mucosa	Colon
31	chr9:116039000-116056800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:116039200-116041200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:116039200-116049400	Strong transcription	Fetal Intestine Small	intestine
35	chr9:116039400-116041200	Genic enhancers	HUVEC	blood vessel
36	chr9:116039400-116051000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr9:116039400-116055200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:116039400-116055800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:116039400-116056200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr9:116039400-116056400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:116039400-116056400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:116039400-116056400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:116039400-116056400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:116039400-116056600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:116039400-116056600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:116039400-116056600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:116039400-116056600	Strong transcription	Placenta	Placenta
50	chr9:116039400-116056600	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links