Variant report

Variant	rs187172
Chromosome Location	chr9:98064431-98064432
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98063794..98065314-chr9:98066856..98068521,2	MCF-7	breast:
2	chr9:98062934..98065072-chr9:98067930..98070513,2	K562	blood:
3	chr9:98064416..98067357-chr9:98070574..98072936,2	K562	blood:
4	chr9:98064416..98068474-chr9:98070574..98074570,5	K562	blood:
5	chr9:98062229..98064595-chr9:98064596..98066110,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10993512	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1125753	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap]
rs171417	1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs184818	1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2404692	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap]
rs356666	0.89[TSI][hapmap];0.91[AMR][1000 genomes]
rs356669	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs356673	1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs356675	0.87[AMR][1000 genomes]
rs356677	1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes]
rs356678	1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes]
rs356679	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs356680	1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs356682	0.85[AMR][1000 genomes]
rs356683	0.87[AMR][1000 genomes]
rs356684	0.87[AMR][1000 genomes]
rs356687	0.83[AMR][1000 genomes]
rs356688	0.87[AMR][1000 genomes]
rs356689	1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs416792	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs437511	0.87[AMR][1000 genomes]
rs4647416	0.82[JPT][hapmap]
rs526189	0.83[AMR][1000 genomes]
rs540412	1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs565293	1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs609324	0.85[AMR][1000 genomes]
rs656939	0.84[ASN][1000 genomes]
rs657637	1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes]
rs944934	1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs187172	SYK	cis	parietal	SCAN
rs187172	C9orf130	cis	parietal	SCAN
rs187172	TDRD7	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98050200-98067400	Weak transcription	A549	lung
2	chr9:98055000-98068600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:98055200-98065600	Weak transcription	Thymus	Thymus
4	chr9:98055400-98066000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:98059600-98067000	Weak transcription	GM12878-XiMat	blood
6	chr9:98059800-98068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:98059800-98068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:98060200-98067400	Weak transcription	HSMM	muscle
9	chr9:98060400-98075000	Weak transcription	NHEK	skin
10	chr9:98061000-98067200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:98061000-98068800	Weak transcription	Small Intestine	intestine
12	chr9:98061800-98067400	Weak transcription	Fetal Lung	lung
13	chr9:98063200-98065800	Weak transcription	Lung	lung
14	chr9:98063200-98068200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:98063400-98068200	Weak transcription	Osteobl	bone
16	chr9:98063400-98069800	Weak transcription	Fetal Kidney	kidney
17	chr9:98063600-98067800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:98063600-98068200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:98063800-98066600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr9:98063800-98066600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr9:98063800-98067400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr9:98064000-98065800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr9:98064000-98067400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:98064000-98068600	Weak transcription	Ovary	ovary
25	chr9:98064200-98065200	Enhancers	NHLF	lung
26	chr9:98064400-98064800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:98064400-98065000	Genic enhancers	Fetal Stomach	stomach
28	chr9:98064400-98065200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr9:98064400-98066200	Enhancers	Fetal Thymus	thymus
30	chr9:98064400-98066400	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links