Variant report

Variant	rs2631694
Chromosome Location	chr15:39989619-39989620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39980861..39985158-chr15:39988045..39992700,5	K562	blood:
2	chr15:39984161..39987304-chr15:39989320..39992486,3	K562	blood:
3	chr15:39976358..39978991-chr15:39987825..39990232,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11070231	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs11854306	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855578	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1320036	0.91[ASN][1000 genomes]
rs1906152	0.80[CEU][hapmap]
rs1906153	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1906156	0.82[EUR][1000 genomes]
rs1906159	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1906160	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2087133	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2129458	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2171310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2254829	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2254942	0.94[ASN][1000 genomes]
rs2254947	0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2411301	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs2411307	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs2412424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2412426	0.81[JPT][hapmap]
rs2631692	0.95[ASN][1000 genomes]
rs2631693	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2631695	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631696	0.94[ASN][1000 genomes]
rs2631697	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs2631698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631702	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2631703	0.91[ASN][1000 genomes]
rs2631705	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2631708	0.93[ASN][1000 genomes]
rs2631709	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2631711	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2631712	0.94[ASN][1000 genomes]
rs2631713	1.00[ASN][1000 genomes]
rs2631715	0.94[ASN][1000 genomes]
rs2664124	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2664126	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2664127	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2664129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2664130	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2664131	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2664132	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2664135	0.83[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3103066	0.95[ASN][1000 genomes]
rs4572354	0.88[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4591113	0.89[CEU][hapmap]
rs4924377	0.89[CEU][hapmap]
rs62004771	0.90[ASN][1000 genomes]
rs62004772	0.95[ASN][1000 genomes]
rs67426899	0.90[ASN][1000 genomes]
rs68183224	0.87[EUR][1000 genomes]
rs7171939	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8028503	0.94[ASN][1000 genomes]
rs8035895	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs937960	0.83[CEU][hapmap];0.85[GIH][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2631694	VPS18	cis	parietal	SCAN
rs2631694	CASC5	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39977200-39990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:39983000-39989800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:39983200-39990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:39985600-39996600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:39985800-39992000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:39985800-39992200	Weak transcription	Fetal Lung	lung
7	chr15:39985800-39996400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:39985800-39996600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:39988000-39996600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:39988200-39990800	Weak transcription	Fetal Intestine Large	intestine
11	chr15:39988800-39990000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:39989200-39990600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:39989400-39989800	Enhancers	Fetal Muscle Leg	muscle
14	chr15:39989400-39991600	Weak transcription	NHDF-Ad	bronchial
15	chr15:39989600-39990600	Enhancers	K562	blood
16	chr15:39989600-39991000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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