Variant report

Variant	rs2728715
Chromosome Location	chr12:32600182-32600183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32550677..32552488-chr12:32597937..32600847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10743793	0.81[AMR][1000 genomes]
rs10771950	0.81[ASN][1000 genomes]
rs10771951	0.81[ASN][1000 genomes]
rs10771952	0.81[ASN][1000 genomes]
rs10771953	0.81[ASN][1000 genomes]
rs10844209	0.81[ASN][1000 genomes]
rs58048246	0.83[AMR][1000 genomes]
rs61927216	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488058	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7297833	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7309975	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7312483	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7314407	0.83[AMR][1000 genomes]
rs7954974	0.83[AMR][1000 genomes]
rs7971819	0.81[ASN][1000 genomes]
rs9634114	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv469347	chr12:32555846-32602079	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv558189	chr12:32555846-32602079	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32592600-32608600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:32594000-32608800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
4	chr12:32595000-32605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:32595800-32604800	Enhancers	HUVEC	blood vessel
6	chr12:32596000-32608800	Weak transcription	Psoas Muscle	Psoas
7	chr12:32596200-32601200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:32596200-32602600	Enhancers	HMEC	breast
9	chr12:32596800-32601000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:32597000-32602600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:32597600-32600200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr12:32597600-32600600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:32597600-32600600	Enhancers	Fetal Intestine Large	intestine
14	chr12:32597600-32600600	Enhancers	Fetal Intestine Small	intestine
15	chr12:32597600-32600800	Enhancers	HepG2	liver
16	chr12:32597600-32601000	Enhancers	Fetal Heart	heart
17	chr12:32597600-32601200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:32597600-32601200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr12:32597600-32601400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:32597600-32602600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:32597800-32601000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:32598200-32606400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:32598400-32602400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr12:32598400-32603600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:32598400-32603800	Weak transcription	HSMM	muscle
26	chr12:32598600-32601200	Enhancers	A549	lung
27	chr12:32598800-32601200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr12:32598800-32601200	Enhancers	Placenta	Placenta
29	chr12:32599400-32600200	Enhancers	Gastric	stomach
30	chr12:32599400-32600400	Enhancers	Hela-S3	cervix
31	chr12:32599400-32601800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:32599600-32601400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:32599600-32601400	Enhancers	Stomach Mucosa	stomach
34	chr12:32599600-32603400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:32599800-32600200	Enhancers	NHLF	lung
36	chr12:32599800-32601000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32599800-32601000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:32599800-32601800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:32599800-32603200	Weak transcription	Small Intestine	intestine
40	chr12:32599800-32605600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:32599800-32605800	Weak transcription	Ovary	ovary
42	chr12:32599800-32608400	Weak transcription	Brain Substantia Nigra	brain
43	chr12:32600000-32601000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:32600000-32601000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:32600000-32601000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:32600000-32601000	Weak transcription	Right Ventricle	heart
47	chr12:32600000-32602000	Enhancers	NHEK	skin
48	chr12:32600000-32602200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:32600000-32602400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:32600000-32603400	Weak transcription	Adipose Nuclei	Adipose

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