Variant report

Variant	rs6479473
Chromosome Location	chr9:96064301-96064302
allele	A/C
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	POLR2A	chr9:96064219-96064396	HepG2	liver:	n/a	n/a
2	CTCF	chr9:96064281-96065514	A549	lung:	n/a	chr9:96065140-96065156 chr9:96064319-96064332 chr9:96064466-96064475 chr9:96065139-96065157

No.	Distal block	Cell Line	Cell type
1	chr9:95960515..95962748-chr9:96063970..96065844,2	MCF-7	breast:
2	chr9:96062175..96064911-chr9:96066749..96068321,2	K562	blood:
3	chr9:96051323..96053243-chr9:96062716..96065079,2	MCF-7	breast:
4	chr9:96054205..96058755-chr9:96061052..96064429,5	MCF-7	breast:
5	chr9:96063114..96067393-chr9:96338286..96340131,3	MCF-7	breast:
6	chr9:95953204..95955785-chr9:96063844..96066566,2	MCF-7	breast:

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000165238	Chromatin interaction
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10733747	0.82[EUR][1000 genomes]
rs10761206	0.82[EUR][1000 genomes]
rs10761208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821104	0.82[EUR][1000 genomes]
rs1111776	0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12683662	0.92[AFR][1000 genomes]
rs12684392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12684553	0.82[EUR][1000 genomes]
rs1343631	0.82[EUR][1000 genomes]
rs1889338	0.92[YRI][hapmap]
rs1891970	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1931366	0.82[EUR][1000 genomes]
rs1931367	0.82[EUR][1000 genomes]
rs1931368	0.82[EUR][1000 genomes]
rs1936401	0.85[EUR][1000 genomes]
rs2151714	0.92[YRI][hapmap]
rs2169756	0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2991376	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2995999	1.00[YRI][hapmap]
rs3001449	0.87[AFR][1000 genomes]
rs3847306	1.00[CEU][hapmap]
rs4548243	0.92[YRI][hapmap]
rs4743908	0.82[EUR][1000 genomes]
rs4743909	0.85[EUR][1000 genomes]
rs4743913	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4743914	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4744210	0.82[EUR][1000 genomes]
rs4744214	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56161352	0.86[AFR][1000 genomes]
rs6479472	0.85[EUR][1000 genomes]
rs7020940	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7021187	0.85[EUR][1000 genomes]
rs7025514	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs7025611	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7031917	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs7042492	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7044229	0.92[AFR][1000 genomes]
rs73651384	0.82[AFR][1000 genomes]
rs7853075	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs7856268	0.85[EUR][1000 genomes]
rs7866298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7872608	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
2	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:96047200-96065000	Weak transcription	Fetal Brain Male	brain
6	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:96052200-96066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:96056800-96067400	Weak transcription	Brain Anterior Caudate	brain
11	chr9:96058200-96064600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:96058200-96064600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:96059600-96067000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr9:96059800-96064600	Strong transcription	Brain Germinal Matrix	brain
15	chr9:96060000-96065000	Enhancers	Colonic Mucosa	Colon
16	chr9:96060000-96066200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:96061000-96065800	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:96061000-96072200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:96061200-96067400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:96061400-96075000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:96061600-96066800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:96061600-96066800	Weak transcription	Left Ventricle	heart
23	chr9:96061600-96067000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:96061600-96070200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:96061600-96079000	Weak transcription	Gastric	stomach
26	chr9:96061800-96065200	Strong transcription	Fetal Stomach	stomach
27	chr9:96061800-96066200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:96062000-96066600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:96062400-96065600	Enhancers	HepG2	liver
30	chr9:96062600-96069200	Enhancers	Fetal Muscle Leg	muscle
31	chr9:96062800-96065000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:96063000-96065200	Enhancers	Spleen	Spleen
33	chr9:96063000-96070200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:96063200-96064600	Weak transcription	Pancreas	Pancrea
35	chr9:96063200-96064800	Weak transcription	Stomach Mucosa	stomach
36	chr9:96063200-96065000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:96063200-96066800	Weak transcription	Psoas Muscle	Psoas
38	chr9:96063200-96072200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:96063400-96064800	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:96063400-96064800	Strong transcription	Fetal Intestine Small	intestine
41	chr9:96063400-96067400	Weak transcription	Adipose Nuclei	Adipose
42	chr9:96063400-96069200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:96063600-96065200	Enhancers	Placenta	Placenta
44	chr9:96063600-96070600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr9:96063800-96064600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr9:96063800-96064800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr9:96063800-96066000	Weak transcription	Fetal Heart	heart
48	chr9:96063800-96067000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr9:96063800-96067400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:96063800-96088600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links