Variant report

Variant	rs17371638
Chromosome Location	chr1:62305995-62305996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12022830	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12029243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12045057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1286816	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17380420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2185136	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2275859	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2788616	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2799629	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs58052322	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58932514	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7515512	1.00[JPT][hapmap]
rs7554677	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[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:68 , 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	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
5	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
6	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:62278200-62316400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
10	chr1:62290600-62308600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:62290800-62326000	Weak transcription	Left Ventricle	heart
12	chr1:62292000-62309200	Weak transcription	Gastric	stomach
13	chr1:62293800-62321600	Weak transcription	Esophagus	oesophagus
14	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:62294400-62330200	Weak transcription	Fetal Stomach	stomach
16	chr1:62294600-62321000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:62294800-62324000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:62295000-62322600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:62295200-62307600	Weak transcription	Aorta	Aorta
20	chr1:62295800-62310800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:62295800-62321600	Weak transcription	Primary T cells from cord blood	blood
22	chr1:62296000-62310800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:62296000-62321400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:62296000-62321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:62296200-62321600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:62297400-62321400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:62297600-62307000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:62297800-62310000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:62297800-62310600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:62297800-62313800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:62297800-62321600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:62298000-62330000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:62300200-62321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:62300600-62310600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:62300800-62310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:62300800-62321400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:62301400-62320800	Weak transcription	Fetal Intestine Small	intestine
38	chr1:62301400-62331400	Weak transcription	Psoas Muscle	Psoas
39	chr1:62302600-62307200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:62302600-62308800	Weak transcription	Brain Anterior Caudate	brain
41	chr1:62302600-62321400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:62302600-62331400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:62303600-62306000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:62303600-62306000	Enhancers	Hela-S3	cervix
45	chr1:62303800-62321600	Weak transcription	Liver	Liver
46	chr1:62304400-62306000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr1:62304600-62306000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:62304600-62306400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:62304600-62306800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:62304800-62306000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links