Variant report

Variant	rs1548620
Chromosome Location	chr7:39789747-39789748
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39785039..39787598-chr7:39788588..39791409,2	K562	blood:
2	chr7:39662331..39664250-chr7:39789665..39791782,2	MCF-7	breast:
3	chr7:39662813..39664349-chr7:39788330..39790585,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11764732	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12701760	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12701761	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12701762	0.87[ASN][1000 genomes]
rs12701763	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13223212	0.86[ASN][1000 genomes]
rs13247273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329526	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6950742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966007	0.89[ASN][1000 genomes]
rs6968962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977471	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7458148	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39774200-39790400	Weak transcription	Fetal Kidney	kidney
2	chr7:39774200-39793400	Weak transcription	Ovary	ovary
3	chr7:39774200-39807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:39774400-39794000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:39774400-39797600	Weak transcription	Thymus	Thymus
6	chr7:39775800-39793400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:39775800-39796400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:39775800-39807000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr7:39775800-39811200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:39776000-39793800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:39776200-39793800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:39776200-39794000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:39776600-39820400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:39776800-39790000	Weak transcription	Dnd41	blood
15	chr7:39781800-39793400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:39782400-39790200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:39782400-39792800	Weak transcription	Fetal Intestine Small	intestine
18	chr7:39782400-39793400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:39782400-39809000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:39784800-39793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:39784800-39793400	Weak transcription	Esophagus	oesophagus
22	chr7:39784800-39802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:39785000-39831800	Weak transcription	Primary B cells from cord blood	blood
24	chr7:39786000-39793800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:39786000-39793800	Weak transcription	Fetal Stomach	stomach
26	chr7:39786600-39793400	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:39787200-39794000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:39787400-39793400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:39787800-39791000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:39787800-39794000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:39788400-39789800	Enhancers	Hela-S3	cervix
32	chr7:39788600-39790000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr7:39788600-39790200	Enhancers	HepG2	liver
34	chr7:39788800-39789800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr7:39788800-39790000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr7:39788800-39790200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr7:39789000-39790000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr7:39789000-39790000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr7:39789000-39790400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr7:39789000-39790800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:39789000-39793400	Weak transcription	NHLF	lung
42	chr7:39789000-39793800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:39789200-39790000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr7:39789200-39794000	Weak transcription	HUVEC	blood vessel
45	chr7:39789400-39791000	Weak transcription	NHDF-Ad	bronchial
46	chr7:39789400-39791800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:39789400-39793400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:39789400-39793800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:39789400-39793800	Weak transcription	NH-A	brain
50	chr7:39789400-39793800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links