Variant report

Variant	rs6479470
Chromosome Location	chr9:96044083-96044084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96028435..96030029-chr9:96043417..96045547,2	MCF-7	breast:
2	chr9:95945010..95947116-chr9:96042384..96044882,2	MCF-7	breast:
3	chr9:96042949..96045930-chr9:96049187..96051253,2	MCF-7	breast:
4	chr9:96043151..96044840-chr9:96069194..96071297,2	K562	blood:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10733747	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761208	0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs10821104	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1111776	0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs12683662	0.88[EUR][1000 genomes]
rs12684392	0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs12684553	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1343631	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1891970	0.94[EUR][1000 genomes]
rs1931365	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1931366	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1931367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1931368	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1936401	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2169756	0.94[EUR][1000 genomes]
rs4147136	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4743908	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743909	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744209	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4744210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744214	0.91[EUR][1000 genomes]
rs6479472	0.94[EUR][1000 genomes]
rs7020940	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7021187	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7042028	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042492	0.97[EUR][1000 genomes]
rs7853075	1.00[CEU][hapmap]
rs7856268	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7866298	0.94[EUR][1000 genomes]
rs7872608	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:96031400-96054600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:96031400-96055000	Weak transcription	Colonic Mucosa	Colon
6	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:96033000-96054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:96033000-96055000	Weak transcription	Brain Anterior Caudate	brain
9	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
10	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:96033600-96044400	Weak transcription	Left Ventricle	heart
14	chr9:96033600-96046000	Weak transcription	Pancreas	Pancrea
15	chr9:96033600-96050200	Weak transcription	Fetal Intestine Small	intestine
16	chr9:96033600-96054600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:96033800-96054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:96035800-96051600	Weak transcription	Fetal Intestine Large	intestine
23	chr9:96040600-96049600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:96041000-96049400	Weak transcription	Brain Germinal Matrix	brain
25	chr9:96041000-96050400	Weak transcription	HepG2	liver
26	chr9:96041000-96052400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:96041400-96046200	Weak transcription	Fetal Brain Female	brain
28	chr9:96041400-96052000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:96041600-96044600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:96041600-96056800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:96041800-96054600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:96042600-96044200	Enhancers	HMEC	breast
33	chr9:96042600-96044400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:96043800-96044200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:96044000-96044800	Enhancers	Fetal Heart	heart

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