Variant report

Variant	rs2158547
Chromosome Location	chr7:39677722-39677723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39661695..39665595-chr7:39674627..39679140,4	MCF-7	breast:
2	chr7:39677650..39680177-chr7:39682752..39684306,2	K562	blood:
3	chr7:39661637..39664462-chr7:39677218..39679783,2	K562	blood:
4	chr7:39670051..39674974-chr7:39675213..39680609,7	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10232064	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11769962	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11769987	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13224312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2008819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35694450	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4723888	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6462938	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6462939	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6948088	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7806633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39664400-39678400	Weak transcription	Placenta	Placenta
2	chr7:39664400-39679600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:39665200-39677800	Weak transcription	Brain Substantia Nigra	brain
4	chr7:39665400-39679800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:39665600-39680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:39665600-39682200	Weak transcription	Liver	Liver
7	chr7:39666200-39678200	Weak transcription	Brain Germinal Matrix	brain
8	chr7:39666200-39679000	Weak transcription	Esophagus	oesophagus
9	chr7:39666200-39681800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:39666200-39694400	Weak transcription	Fetal Brain Female	brain
11	chr7:39666800-39681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:39667200-39698800	Weak transcription	Fetal Kidney	kidney
13	chr7:39667600-39678800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:39668200-39681000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:39668200-39681000	Weak transcription	Fetal Heart	heart
16	chr7:39668600-39680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:39669600-39681200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:39671800-39679600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:39671800-39679800	Weak transcription	Ovary	ovary
20	chr7:39671800-39693800	Weak transcription	A549	lung
21	chr7:39672200-39679200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:39672200-39679200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:39672200-39679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:39672200-39681600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:39672200-39681800	Weak transcription	Gastric	stomach
26	chr7:39672200-39681800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:39672200-39684000	Weak transcription	NHLF	lung
28	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
29	chr7:39672400-39683200	Weak transcription	Pancreas	Pancrea
30	chr7:39672800-39679600	Weak transcription	Aorta	Aorta
31	chr7:39672800-39680400	Weak transcription	K562	blood
32	chr7:39672800-39681800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:39673400-39679600	Weak transcription	Brain Angular Gyrus	brain
34	chr7:39673600-39678400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:39673600-39679000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:39673600-39679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:39674000-39678200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:39674000-39678200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:39674000-39678200	Weak transcription	Left Ventricle	heart
40	chr7:39674000-39678400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:39674000-39678400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:39674000-39679000	Weak transcription	Adipose Nuclei	Adipose
43	chr7:39674000-39679000	Weak transcription	Right Ventricle	heart
44	chr7:39674000-39679000	Weak transcription	NHEK	skin
45	chr7:39674000-39681600	Weak transcription	Fetal Lung	lung
46	chr7:39674000-39690200	Weak transcription	NH-A	brain
47	chr7:39674000-39690800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:39674200-39677800	Weak transcription	Fetal Muscle Leg	muscle
49	chr7:39674200-39678200	Weak transcription	Fetal Thymus	thymus
50	chr7:39674200-39678400	Strong transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links