Variant report

Variant	rs6479494
Chromosome Location	chr9:96330499-96330500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:96330444-96331049	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:96328571-96330906	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:96330473-96331070	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96286264..96288852-chr9:96329560..96332298,3	MCF-7	breast:
2	chr9:96210381..96218248-chr9:96327402..96333234,10	MCF-7	breast:
3	chr9:96329551..96331505-chr9:96420260..96423135,2	MCF-7	breast:
4	chr9:96208657..96210806-chr9:96328635..96330636,2	K562	blood:
5	chr9:96213362..96216144-chr9:96327494..96330556,6	K562	blood:
6	chr9:96318350..96320504-chr9:96329383..96332231,2	MCF-7	breast:
7	chr9:96205732..96207366-chr9:96330397..96333362,2	MCF-7	breast:
8	chr9:96328888..96330785-chr9:96400006..96401542,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263875	TF binding region
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10046907	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10429558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761236	0.82[ASN][1000 genomes]
rs11975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554020	0.81[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1331588	0.83[LWK][hapmap]
rs3815563	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4552973	0.81[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59483310	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59582399	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60076242	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479482	0.85[EUR][1000 genomes]
rs6479483	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6479487	0.86[AMR][1000 genomes]
rs6479495	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020459	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7023933	0.85[AMR][1000 genomes]
rs7025805	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7028729	0.85[EUR][1000 genomes]
rs7035657	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs7036984	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7038564	0.88[ASW][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7048853	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7850322	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7853605	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes]
rs7857183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859267	0.84[CHB][hapmap]
rs7860098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862998	0.85[EUR][1000 genomes]
rs7870210	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6479494	RP11-165J3.6	cis	Thyroid	GTEx
rs6479494	FAM120AOS	cis	cerebellum	SCAN
rs6479494	ANKRD19	cis	cerebellum	SCAN
rs6479494	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs6479494	RP11-165J3.6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96329600-96330800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:96329600-96331000	Enhancers	Placenta	Placenta
3	chr9:96329600-96331000	Enhancers	Gastric	stomach
4	chr9:96329600-96331200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:96329600-96332200	Enhancers	Spleen	Spleen
6	chr9:96329800-96330800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:96329800-96330800	Enhancers	Pancreas	Pancrea
8	chr9:96329800-96331000	Enhancers	Fetal Thymus	thymus
9	chr9:96329800-96333000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:96330000-96330800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr9:96330000-96331200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:96330000-96331800	Weak transcription	Thymus	Thymus
13	chr9:96330000-96332000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:96330000-96332600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:96330000-96333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:96330000-96333200	Weak transcription	A549	lung
17	chr9:96330000-96337200	Weak transcription	NHLF	lung
18	chr9:96330000-96337400	Weak transcription	Hela-S3	cervix
19	chr9:96330000-96337400	Weak transcription	HSMM	muscle
20	chr9:96330200-96330600	Weak transcription	Fetal Stomach	stomach
21	chr9:96330200-96330800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:96330200-96331000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr9:96330200-96331400	Weak transcription	Primary B cells from cord blood	blood
24	chr9:96330200-96331400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:96330200-96331600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr9:96330200-96331600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:96330200-96331800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:96330200-96331800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:96330200-96331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:96330200-96332000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:96330200-96332600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:96330200-96332800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:96330200-96332800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:96330200-96332800	Weak transcription	Fetal Brain Female	brain
35	chr9:96330200-96333000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:96330200-96333000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:96330200-96333200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:96330200-96333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:96330200-96333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:96330200-96335200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:96330200-96335200	Weak transcription	Left Ventricle	heart
42	chr9:96330200-96335600	Weak transcription	Esophagus	oesophagus
43	chr9:96330200-96336400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:96330200-96336400	Weak transcription	Brain Substantia Nigra	brain
45	chr9:96330200-96336600	Weak transcription	Primary T cells from cord blood	blood
46	chr9:96330200-96336600	Weak transcription	Lung	lung
47	chr9:96330200-96336800	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:96330200-96336800	Weak transcription	Fetal Lung	lung
49	chr9:96330200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:96330200-96337000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links