Variant report

Variant	rs6475949
Chromosome Location	chr9:2702351-2702352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2697672..2699456-chr9:2700934..2702755,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10967598	0.83[AMR][1000 genomes]
rs12686646	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1454630	0.88[ASN][1000 genomes]
rs1884441	0.87[AMR][1000 genomes]
rs1889109	0.86[AMR][1000 genomes]
rs59115139	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7853868	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892078	chr9:2668085-2705874	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv466084	chr9:2681397-2710537	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv613138	chr9:2681397-2710537	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv531565	chr9:2682523-2784028	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv613139	chr9:2689244-2710537	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv466085	chr9:2690980-2710537	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv466086	chr9:2690980-2710537	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv613140	chr9:2690980-2710537	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv471270	chr9:2690980-2711636	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv613141	chr9:2690980-2711637	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv516425	chr9:2690980-2790307	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv892080	chr9:2691186-2721249	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv1030063	chr9:2691667-2729595	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv1032667	chr9:2691667-2788242	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1019973	chr9:2691812-2790419	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv539935	chr9:2691812-2790419	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv973427	chr9:2699385-2709019	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2688600-2702400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:2690000-2702600	Weak transcription	Primary T cells from cord blood	blood
3	chr9:2690600-2718000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:2691200-2710600	Weak transcription	Left Ventricle	heart
5	chr9:2692000-2709600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:2697200-2722800	Weak transcription	HSMM	muscle
7	chr9:2698000-2717600	Weak transcription	Esophagus	oesophagus
8	chr9:2700600-2702400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:2700600-2727800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:2701400-2702400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:2701600-2702400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:2701600-2702400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:2701600-2702800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:2701600-2727800	Weak transcription	Pancreas	Pancrea
15	chr9:2702000-2703000	Enhancers	Fetal Heart	heart
16	chr9:2702000-2709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:2702000-2721400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:2702200-2703200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:2702200-2711600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:2702200-2722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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