Variant report

Variant	rs6832090
Chromosome Location	chr4:48040791-48040792
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	chr4:48040732..48041262-chr4:48049418..48050146,3	MCF-7	breast:
2	chr4:48040732..48041255-chr4:48049418..48050146,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1507923	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860943	1.00[YRI][hapmap]
rs1979972	1.00[YRI][hapmap]
rs2251240	1.00[YRI][hapmap]
rs2352588	0.81[AFR][1000 genomes]
rs2352591	0.85[YRI][hapmap]
rs2464500	1.00[YRI][hapmap]
rs2581495	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2661545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2704428	0.92[YRI][hapmap]
rs2704432	1.00[YRI][hapmap]
rs2882951	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs321629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs321648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6825478	1.00[AMR][1000 genomes]
rs6830656	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv967990	chr4:48037803-48041600	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
3	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
4	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48028200-48040800	Weak transcription	Gastric	stomach
7	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
8	chr4:48031600-48041800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
12	chr4:48034800-48041600	Strong transcription	HMEC	breast
13	chr4:48036200-48041000	Enhancers	Primary B cells from cord blood	blood
14	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:48038000-48042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:48038000-48044600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:48038000-48044800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:48038000-48047800	Weak transcription	NHEK	skin
19	chr4:48038200-48044400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:48038200-48045200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:48038400-48044600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:48038600-48043600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:48038600-48045200	Weak transcription	Fetal Heart	heart
24	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:48039000-48045400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:48039400-48043800	Enhancers	GM12878-XiMat	blood
27	chr4:48039400-48044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:48039600-48044800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:48040000-48041800	Enhancers	HepG2	liver
30	chr4:48040200-48041200	Enhancers	Liver	Liver
31	chr4:48040400-48041000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr4:48040400-48041000	Enhancers	Fetal Intestine Small	intestine
33	chr4:48040400-48044400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links