Variant report

Variant	rs16969640
Chromosome Location	chr15:39996874-39996875
allele	C/G
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: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1004739	0.89[CHB][hapmap];0.84[CHD][hapmap]
rs1004740	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs10459607	0.94[JPT][hapmap]
rs11631570	0.81[CHB][hapmap];0.82[JPT][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];0.96[EUR][1000 genomes]
rs11856294	0.89[CHB][hapmap]
rs11856448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857927	0.89[CHB][hapmap]
rs12911842	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs1320036	0.96[EUR][1000 genomes]
rs16969445	0.88[CHB][hapmap]
rs16969460	0.82[CHB][hapmap]
rs16969478	1.00[MEX][hapmap]
rs16969637	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];0.80[EUR][1000 genomes]
rs1876853	0.89[MEX][hapmap]
rs1906153	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs1906159	0.90[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs1906160	0.90[CEU][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs2008623	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087132	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2129458	0.80[EUR][1000 genomes]
rs2254829	0.81[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2254942	0.98[EUR][1000 genomes]
rs2254947	0.96[EUR][1000 genomes]
rs2412409	0.82[CHB][hapmap]
rs2412413	0.89[MEX][hapmap]
rs2412424	0.80[EUR][1000 genomes]
rs2631692	0.98[EUR][1000 genomes]
rs2631693	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs2631695	0.81[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2631696	0.98[EUR][1000 genomes]
rs2631698	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs2631703	0.96[EUR][1000 genomes]
rs2631708	0.80[EUR][1000 genomes]
rs2631709	0.80[EUR][1000 genomes]
rs2631712	0.80[EUR][1000 genomes]
rs2631715	0.88[EUR][1000 genomes]
rs2664124	0.80[EUR][1000 genomes]
rs2664127	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs2664130	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs2664131	0.81[CEU][hapmap];0.98[EUR][1000 genomes]
rs2898687	0.89[MEX][hapmap]
rs3103066	0.98[EUR][1000 genomes]
rs4476147	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs56197892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004766	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004768	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62004771	0.96[EUR][1000 genomes]
rs62004772	0.98[EUR][1000 genomes]
rs67426899	0.96[EUR][1000 genomes]
rs7162070	0.89[MEX][hapmap]
rs7162781	0.89[MEX][hapmap]
rs8028503	0.91[EUR][1000 genomes]
rs8029602	0.89[MEX][hapmap]
rs8035895	0.80[EUR][1000 genomes]
rs884584	0.89[MEX][hapmap]
rs951358	0.81[CEU][hapmap];0.81[EUR][1000 genomes]

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
rs16969640	RTF1	cis	parietal	SCAN
rs16969640	FSIP1	cis	parietal	SCAN
rs16969640	THBS1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

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

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