Variant report

Variant	rs11139569
Chromosome Location	chr9:85051706-85051707
allele	A/G
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	FOS	chr9:85051421-85051709	MCF10A-Er-Src	breast:	n/a	chr9:85051572-85051580
2	FOS	chr9:85051367-85051738	MCF10A-Er-Src	breast:	n/a	chr9:85051572-85051580
3	FOS	chr9:85051352-85051728	MCF10A-Er-Src	breast:	n/a	chr9:85051572-85051580
4	STAT3	chr9:85051308-85051731	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr9:85051392-85051818	IMR90	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM75B-4	chr9:85051617-85052093	expReg_chr9_3630_-

Variant related genes	Relation type
ENSG00000228123	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10125999	0.82[CEU][hapmap]
rs1041392	0.94[ASN][1000 genomes]
rs11139564	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11139570	0.95[ASN][1000 genomes]
rs12350753	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683121	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12683715	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12684844	0.94[ASN][1000 genomes]
rs12685162	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13290374	0.83[ASN][1000 genomes]
rs13298628	0.87[ASN][1000 genomes]
rs13299917	0.81[ASN][1000 genomes]
rs1330817	0.80[ASN][1000 genomes]
rs1411660	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1411661	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1411662	0.96[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs17085530	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17085531	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026194	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2378631	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2889949	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34637520	0.95[ASN][1000 genomes]
rs34845422	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34867546	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35089927	0.89[ASN][1000 genomes]
rs35501117	0.91[ASN][1000 genomes]
rs35576282	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35677430	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3892417	0.82[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs4465043	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4478643	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4877232	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4877233	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4877692	0.95[ASN][1000 genomes]
rs4877693	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs56291243	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67968529	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7018522	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021813	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7036901	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037151	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7046852	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7048952	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7850032	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7850751	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7854052	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs7865259	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7865649	0.97[ASN][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	nsv893507	chr9:84799537-85097651	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893508	chr9:84954592-85080395	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893509	chr9:84954592-85097651	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893510	chr9:84954592-85117420	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv982311	chr9:85041031-85052919	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv982541	chr9:85048466-85052919	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85051400-85051800	Enhancers	Osteobl	bone
2	chr9:85051400-85052000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:85051400-85052600	Enhancers	NHEK	skin
4	chr9:85051600-85052000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr9:85051600-85052000	Enhancers	NH-A	brain
6	chr9:85051600-85052400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:85051600-85052400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:85051600-85052400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:85051600-85053400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:85051600-85054000	Enhancers	HMEC	breast

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