Variant report

Variant	rs1572670
Chromosome Location	chr1:62306819-62306820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:62188330..62190848-chr1:62304902..62307738,2	K562	blood:
2	chr1:62208685..62210922-chr1:62306053..62308101,2	MCF-7	breast:
3	chr1:62304428..62307569-chr1:62310144..62313240,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162604	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11207848	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1286813	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2788615	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2799625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2799629	0.80[YRI][hapmap]
rs2811325	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4456122	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs6587948	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1099	chr1:62275317-62315943	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
3	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
4	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
5	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:62278200-62316400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
9	chr1:62290600-62308600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:62290800-62326000	Weak transcription	Left Ventricle	heart
11	chr1:62292000-62309200	Weak transcription	Gastric	stomach
12	chr1:62293800-62321600	Weak transcription	Esophagus	oesophagus
13	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:62294400-62330200	Weak transcription	Fetal Stomach	stomach
15	chr1:62294600-62321000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62294800-62324000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:62295000-62322600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:62295200-62307600	Weak transcription	Aorta	Aorta
19	chr1:62295800-62310800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:62295800-62321600	Weak transcription	Primary T cells from cord blood	blood
21	chr1:62296000-62310800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:62296000-62321400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:62296000-62321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:62296200-62321600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:62297400-62321400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:62297600-62307000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:62297800-62310000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:62297800-62310600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:62297800-62313800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:62297800-62321600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:62298000-62330000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:62300200-62321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:62300600-62310600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:62300800-62310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:62300800-62321400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:62301400-62320800	Weak transcription	Fetal Intestine Small	intestine
37	chr1:62301400-62331400	Weak transcription	Psoas Muscle	Psoas
38	chr1:62302600-62307200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:62302600-62308800	Weak transcription	Brain Anterior Caudate	brain
40	chr1:62302600-62321400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:62302600-62331400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:62303800-62321600	Weak transcription	Liver	Liver
43	chr1:62305000-62307800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:62305000-62309000	Weak transcription	Brain Angular Gyrus	brain
45	chr1:62305200-62307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:62305600-62310600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:62305600-62320800	Weak transcription	HMEC	breast
48	chr1:62305600-62321600	Weak transcription	NHEK	skin
49	chr1:62305800-62308400	Weak transcription	Stomach Mucosa	stomach
50	chr1:62305800-62312400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links