Variant report

Variant	rs9684012
Chromosome Location	chr4:148897030-148897031
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	chr4:148881694..148883564-chr4:148895633..148897317,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10002792	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10025180	0.85[ASN][1000 genomes]
rs1039660	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10519926	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519933	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs11945457	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13435037	0.82[CEU][hapmap]
rs17024212	0.82[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17024235	0.92[CHD][hapmap]
rs2262881	0.87[ASW][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs2306910	0.82[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2635259	0.80[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs35133175	0.84[CHD][hapmap]
rs56834952	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57437177	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60635047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535571	0.82[CEU][hapmap]
rs6811259	0.82[CEU][hapmap]
rs6856135	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs7674116	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682961	0.82[AMR][1000 genomes];0.81[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	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3398182	chr4:148895102-148898800	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148859400-148898000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
3	chr4:148868200-148902600	Weak transcription	NH-A	brain
4	chr4:148885600-148905200	Weak transcription	Fetal Intestine Small	intestine
5	chr4:148885600-148905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:148885600-148939000	Weak transcription	Pancreas	Pancrea
7	chr4:148885800-148907000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:148885800-148912800	Weak transcription	Fetal Lung	lung
9	chr4:148886000-148917600	Weak transcription	Esophagus	oesophagus
10	chr4:148886800-148901800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:148889000-148905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:148889200-148899400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:148889200-148936200	Weak transcription	Fetal Intestine Large	intestine
14	chr4:148889400-148905400	Weak transcription	NHLF	lung
15	chr4:148890400-148897800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:148891400-148905000	Weak transcription	Stomach Mucosa	stomach
17	chr4:148891400-148905400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:148891600-148905400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:148891600-148912800	Weak transcription	Fetal Kidney	kidney
20	chr4:148891600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:148891600-148928000	Weak transcription	A549	lung
22	chr4:148891800-148901600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:148892000-148898200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:148892800-148897200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:148893800-148901800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:148893800-148901800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:148896000-148897200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:148896000-148898000	Enhancers	NHDF-Ad	bronchial
29	chr4:148896200-148897200	Genic enhancers	HSMM	muscle
30	chr4:148896200-148897400	Enhancers	Psoas Muscle	Psoas
31	chr4:148896200-148897600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:148896200-148898000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:148896200-148898200	Enhancers	Colon Smooth Muscle	Colon
34	chr4:148896200-148898200	Enhancers	HSMMtube	muscle
35	chr4:148896200-148898800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:148896400-148897200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:148896400-148897200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:148896400-148897200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr4:148896400-148897200	Genic enhancers	Fetal Muscle Leg	muscle
40	chr4:148896400-148897200	Enhancers	Gastric	stomach
41	chr4:148896400-148897200	Enhancers	Left Ventricle	heart
42	chr4:148896400-148897200	Genic enhancers	Lung	lung
43	chr4:148896400-148897200	Enhancers	Right Atrium	heart
44	chr4:148896400-148897200	Enhancers	Right Ventricle	heart
45	chr4:148896400-148897400	Enhancers	Adipose Nuclei	Adipose
46	chr4:148896400-148897600	Enhancers	Fetal Stomach	stomach
47	chr4:148896400-148897600	Enhancers	Ovary	ovary
48	chr4:148896400-148897600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr4:148896400-148897800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:148896400-148897800	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links