Variant report

Variant	rs16972996
Chromosome Location	chr17:66512084-66512085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66507070..66510931-chr17:66511371..66513422,6	K562	blood:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10468444	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491176	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];1.00[EUR][1000 genomes]
rs10852738	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs16973034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302235	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736761	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56112060	0.82[ASN][1000 genomes]
rs7221724	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847781	0.85[ASN][1000 genomes]
rs72847782	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847784	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847785	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847789	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847790	1.00[EUR][1000 genomes]
rs72847794	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847801	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74000753	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067357	0.82[ASN][1000 genomes]
rs8072598	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv932935	chr17:66511434-66518806	Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv933839	chr17:66511434-66518903	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16972996	PRKAR1A	cis	multi-tissue	Pritchard
rs16972996	PITPNC1	cis	cerebellum	SCAN
rs16972996	WIPI1	cis	multi-tissue	Pritchard
rs16972996	AMZ2P1	cis	parietal	SCAN
rs16972996	WIPI1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66507400-66513600	Active TSS	Right Ventricle	heart
2	chr17:66509600-66513000	Weak transcription	Spleen	Spleen
3	chr17:66509600-66513400	Weak transcription	Gastric	stomach
4	chr17:66509600-66513600	Weak transcription	Esophagus	oesophagus
5	chr17:66509600-66525800	Weak transcription	Pancreas	Pancrea
6	chr17:66509800-66514200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:66510000-66513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:66510200-66512800	Weak transcription	Colonic Mucosa	Colon
9	chr17:66510200-66513400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:66511200-66512200	Genic enhancers	Fetal Lung	lung
11	chr17:66511200-66512800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:66511200-66513200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:66511200-66513400	Weak transcription	Fetal Intestine Small	intestine
14	chr17:66511200-66514000	Strong transcription	K562	blood
15	chr17:66511200-66514200	Strong transcription	Placenta	Placenta
16	chr17:66511200-66515400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr17:66511200-66516800	Strong transcription	Fetal Thymus	thymus
18	chr17:66511400-66512200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:66511400-66512200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:66511400-66512400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:66511400-66512400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr17:66511400-66512600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:66511400-66512800	Weak transcription	Primary T cells from cord blood	blood
24	chr17:66511400-66512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr17:66511400-66513000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr17:66511400-66513000	Weak transcription	Brain Germinal Matrix	brain
27	chr17:66511400-66513400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:66511400-66513800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:66511400-66514200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:66511400-66514200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr17:66511400-66514200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr17:66511400-66514600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:66511400-66514800	Strong transcription	Dnd41	blood
34	chr17:66511400-66515000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
35	chr17:66511400-66516200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:66511400-66516400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr17:66511400-66516600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr17:66511600-66512400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:66511600-66512400	Enhancers	Colon Smooth Muscle	Colon
40	chr17:66511600-66512400	Enhancers	Fetal Heart	heart
41	chr17:66511600-66512600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:66511600-66512600	Weak transcription	Fetal Kidney	kidney
43	chr17:66511600-66513000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:66511600-66513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:66511600-66513000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:66511600-66513200	Weak transcription	Stomach Mucosa	stomach
47	chr17:66511600-66513200	Genic enhancers	NHDF-Ad	bronchial
48	chr17:66511600-66513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:66511600-66514200	Genic enhancers	HepG2	liver
50	chr17:66511600-66514600	Strong transcription	Primary B cells from cord blood	blood

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