Variant report

Variant	rs16969637
Chromosome Location	chr15:39996744-39996745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39989762..39992879-chr15:39994931..39996889,3	K562	blood:
2	chr12:56989910..56991430-chr15:39994772..39997768,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1004739	0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap]
rs1004740	0.89[CHB][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap]
rs10459607	0.94[JPT][hapmap]
rs11631570	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11633974	0.89[CHB][hapmap]
rs11638041	0.88[CHB][hapmap]
rs11638500	0.89[CHB][hapmap]
rs11854797	0.88[CHB][hapmap]
rs11855578	0.81[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs11856294	0.89[CHB][hapmap]
rs11856448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857927	0.89[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12911842	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1320036	0.92[EUR][1000 genomes]
rs16969445	0.88[CHB][hapmap]
rs16969460	0.82[CHB][hapmap]
rs16969475	0.89[MEX][hapmap]
rs16969478	0.88[MEX][hapmap]
rs16969640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17714733	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1876853	1.00[MEX][hapmap]
rs1906153	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs1906159	0.90[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs1906160	0.90[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2008623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087132	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254829	0.81[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2254942	0.91[EUR][1000 genomes]
rs2254947	0.90[EUR][1000 genomes]
rs2412409	0.82[CHB][hapmap]
rs2412413	1.00[MEX][hapmap]
rs2631692	0.91[EUR][1000 genomes]
rs2631693	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs2631695	0.81[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2631696	0.91[EUR][1000 genomes]
rs2631698	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs2631703	0.92[EUR][1000 genomes]
rs2631715	0.82[EUR][1000 genomes]
rs2664127	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs2664130	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs2664131	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs2898687	1.00[MEX][hapmap]
rs3103066	0.91[EUR][1000 genomes]
rs35754803	0.83[AFR][1000 genomes]
rs4476147	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap]
rs56197892	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58332880	0.83[AFR][1000 genomes]
rs62004766	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004768	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62004771	0.92[EUR][1000 genomes]
rs62004772	0.91[EUR][1000 genomes]
rs67426899	0.92[EUR][1000 genomes]
rs7162070	1.00[MEX][hapmap]
rs7162781	1.00[MEX][hapmap]
rs8028503	0.85[EUR][1000 genomes]
rs8029602	1.00[MEX][hapmap]
rs884584	1.00[MEX][hapmap]
rs951358	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16969637	THBS1	cis	parietal	SCAN
rs16969637	FSIP1	cis	parietal	SCAN
rs16969637	RTF1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39993200-39996800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:39994200-39999400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:39994200-39999600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:39995000-39996800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:39996200-39997400	Enhancers	K562	blood
6	chr15:39996400-39997400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr15:39996400-39997400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr15:39996600-39996800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:39996600-39997000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:39996600-39997000	Enhancers	Brain Anterior Caudate	brain
11	chr15:39996600-39997000	Enhancers	Placenta	Placenta
12	chr15:39996600-39997200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr15:39996600-39997200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr15:39996600-39997200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:39996600-39997400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:39996600-39997400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr15:39996600-39997400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr15:39996600-39997400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:39996600-39997400	Enhancers	NHDF-Ad	bronchial
20	chr15:39996600-39997600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:39996600-39997600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:39996600-39997600	Enhancers	Osteobl	bone
23	chr15:39996600-39997800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links