Variant report

Variant	rs1332633
Chromosome Location	chr1:62498141-62498142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12087018	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs12098048	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1332630	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13374203	0.88[CEU][hapmap]
rs1412621	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183996	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365741	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476181	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2476185	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2498981	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2498982	0.88[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4072368	0.87[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4316389	0.81[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4915602	0.87[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6689358	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7515090	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517333	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7520924	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526522	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537239	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7537323	0.86[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][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	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
2	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
3	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
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1332633	AK4	cis	cerebellum	SCAN
rs1332633	NFIA	cis	cerebellum	SCAN
rs1332633	DAB1	cis	parietal	SCAN
rs1332633	INADL	cis	cerebellum	SCAN
rs1332633	OMA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62459200-62511200	Weak transcription	Gastric	stomach
6	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:62460200-62516000	Weak transcription	HMEC	breast
11	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:62484600-62506000	Weak transcription	NHEK	skin
17	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:62488400-62521200	Weak transcription	Ovary	ovary
20	chr1:62488600-62499000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:62490600-62499200	Weak transcription	Right Atrium	heart
22	chr1:62491800-62499200	Weak transcription	Left Ventricle	heart
23	chr1:62491800-62511200	Weak transcription	Psoas Muscle	Psoas
24	chr1:62494600-62504600	Weak transcription	Aorta	Aorta
25	chr1:62494600-62511200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
28	chr1:62494800-62498400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:62494800-62498600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:62494800-62505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:62495000-62499000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:62495000-62504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:62495000-62515200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:62495200-62516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:62495200-62544800	Weak transcription	Liver	Liver
36	chr1:62496200-62504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:62496600-62500400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:62497200-62515000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:62497400-62500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:62497600-62498400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:62497600-62500200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:62497800-62499400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:62497800-62500400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:62498000-62498200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:62498000-62498400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:62498000-62498600	Enhancers	Fetal Heart	heart
47	chr1:62498000-62499000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:62498000-62499000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:62498000-62499200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:62498000-62499200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links