Variant report

Variant	rs28413975
Chromosome Location	chr2:190242788-190242789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190238500..190240603-chr2:190242623..190245183,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10177513	0.81[EUR][1000 genomes]
rs10497699	0.84[ASN][1000 genomes]
rs10931402	0.81[ASN][1000 genomes]
rs10931406	0.81[ASN][1000 genomes]
rs10931410	0.81[ASN][1000 genomes]
rs11675295	0.81[ASN][1000 genomes]
rs11677073	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678388	0.84[ASN][1000 genomes]
rs11681937	0.93[ASN][1000 genomes]
rs11684417	0.93[ASN][1000 genomes]
rs11684869	0.81[ASN][1000 genomes]
rs11687908	0.81[ASN][1000 genomes]
rs11693810	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12472232	0.87[ASN][1000 genomes]
rs1515875	0.83[ASN][1000 genomes]
rs1519185	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520862	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17198815	0.81[ASN][1000 genomes]
rs17198829	0.81[ASN][1000 genomes]
rs17270973	0.84[ASN][1000 genomes]
rs17271008	0.87[ASN][1000 genomes]
rs17271015	0.93[ASN][1000 genomes]
rs1996576	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683013	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683014	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35598715	0.81[ASN][1000 genomes]
rs56252219	0.87[ASN][1000 genomes]
rs56381644	0.93[ASN][1000 genomes]
rs59031473	0.81[ASN][1000 genomes]
rs61410845	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61528955	0.93[ASN][1000 genomes]
rs62182060	0.93[ASN][1000 genomes]
rs62182061	0.93[ASN][1000 genomes]
rs62182066	0.93[ASN][1000 genomes]
rs62182067	0.81[EUR][1000 genomes]
rs62182068	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62182069	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62182070	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62182421	0.81[ASN][1000 genomes]
rs62183794	0.81[ASN][1000 genomes]
rs62183841	0.81[ASN][1000 genomes]
rs62183844	0.81[ASN][1000 genomes]
rs62183845	0.81[ASN][1000 genomes]
rs62183846	0.93[ASN][1000 genomes]
rs62183847	0.85[ASN][1000 genomes]
rs62183848	0.93[ASN][1000 genomes]
rs72912280	0.93[ASN][1000 genomes]
rs72912286	0.93[ASN][1000 genomes]
rs72914135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72914141	0.93[ASN][1000 genomes]
rs72914144	0.80[ASN][1000 genomes]
rs7564429	0.93[ASN][1000 genomes]
rs7586853	0.87[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3451292	chr2:190225623-190266276	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv963941	chr2:190238972-190244573	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190235000-190243800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:190235400-190243800	Weak transcription	Aorta	Aorta
3	chr2:190235800-190243600	Weak transcription	NHLF	lung
4	chr2:190236000-190243600	Weak transcription	NH-A	brain
5	chr2:190236000-190243800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:190236000-190243800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:190236400-190243600	Weak transcription	HSMM	muscle
8	chr2:190238800-190243600	Weak transcription	NHDF-Ad	bronchial
9	chr2:190238800-190243800	Weak transcription	HMEC	breast
10	chr2:190239400-190243800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:190240600-190243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:190240800-190243600	Weak transcription	Osteobl	bone
13	chr2:190240800-190243800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:190241000-190243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:190241000-190243800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:190241200-190243600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:190241400-190243600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:190241400-190243600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:190241600-190243600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:190241600-190243800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:190241800-190242800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:190241800-190243800	Weak transcription	HSMMtube	muscle
23	chr2:190242200-190243600	Weak transcription	NHEK	skin
24	chr2:190242200-190243800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:190242400-190243600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:190242400-190243600	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links