Variant report

Variant	rs7876041
Chromosome Location	chr9:12723530-12723531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12723451..12724539-chr9:12884675..12885414,3	MCF-7	breast:
2	chr9:12723429..12724424-chr9:12884471..12885741,6	MCF-7	breast:
3	chr9:12722041..12725292-chr9:12774361..12778280,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction
ENSG00000222658	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10960766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10960767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10960768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11787674	0.95[EUR][1000 genomes]
rs11787999	0.98[EUR][1000 genomes]
rs11788192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11789339	0.93[EUR][1000 genomes]
rs11789481	0.88[EUR][1000 genomes]
rs11789805	0.93[EUR][1000 genomes]
rs11791497	0.93[EUR][1000 genomes]
rs11791954	0.95[EUR][1000 genomes]
rs11793178	0.93[EUR][1000 genomes]
rs11794050	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11794202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12005881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929383	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929385	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929391	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929400	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16929473	0.86[EUR][1000 genomes]
rs17280279	0.93[EUR][1000 genomes]
rs17280629	0.98[EUR][1000 genomes]
rs17346748	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2209278	0.98[EUR][1000 genomes]
rs34509359	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35238630	0.93[EUR][1000 genomes]
rs35852762	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35866166	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3891858	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41306290	0.98[EUR][1000 genomes]
rs61758391	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61758394	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62638049	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7025758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7026121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7026199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030751	0.95[EUR][1000 genomes]
rs7033962	0.95[EUR][1000 genomes]
rs7035710	0.86[EUR][1000 genomes]
rs7040346	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7041590	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507329	0.80[EUR][1000 genomes]
rs73402088	0.86[EUR][1000 genomes]
rs73402092	0.86[EUR][1000 genomes]
rs768617	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7875424	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12719200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:12720800-12724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:12721400-12723800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:12721600-12723800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:12722000-12723800	Enhancers	Osteobl	bone
6	chr9:12722400-12723600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:12722400-12723800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:12722600-12725000	Enhancers	A549	lung
9	chr9:12722800-12723800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:12722800-12723800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:12722800-12723800	Enhancers	NHDF-Ad	bronchial
12	chr9:12722800-12724400	Enhancers	NHEK	skin
13	chr9:12723000-12725000	Enhancers	Fetal Lung	lung
14	chr9:12723200-12723600	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:12723200-12723800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:12723200-12723800	Enhancers	Colon Smooth Muscle	Colon
17	chr9:12723200-12723800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr9:12723200-12723800	Enhancers	HMEC	breast
19	chr9:12723400-12723800	Enhancers	NHLF	lung

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