Variant report

Variant	rs7171939
Chromosome Location	chr15:40022773-40022774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40022385..40024167-chr15:40025741..40027363,2	K562	blood:
2	chr15:40021204..40023885-chr15:40025697..40027241,2	K562	blood:
3	chr15:40021277..40023471-chr15:40056551..40058310,2	MCF-7	breast:
4	chr15:40022589..40023089-chr6:3118787..3119378,2	NB4	blood:

Variant related genes	Relation type
ENSG00000137274	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11070231	0.90[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11854306	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11855578	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1320036	0.94[ASN][1000 genomes]
rs1906153	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1906159	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1906160	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2087133	0.89[ASN][1000 genomes]
rs2129458	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2171310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254829	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2254942	0.91[ASN][1000 genomes]
rs2254947	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2412424	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2412426	0.81[JPT][hapmap]
rs2631692	0.89[ASN][1000 genomes]
rs2631693	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2631694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631695	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631696	0.91[ASN][1000 genomes]
rs2631698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631702	0.81[ASW][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap]
rs2631703	0.94[ASN][1000 genomes]
rs2631705	0.81[ASW][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap]
rs2631708	0.87[ASN][1000 genomes]
rs2631709	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631711	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631712	0.89[ASN][1000 genomes]
rs2631713	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631715	0.88[ASN][1000 genomes]
rs2664124	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2664126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2664127	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2664129	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2664130	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2664131	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2664132	0.94[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2664135	0.82[GIH][hapmap];0.92[MKK][hapmap]
rs3103065	0.81[CEU][hapmap]
rs3103066	0.89[ASN][1000 genomes]
rs4429263	0.83[GIH][hapmap]
rs4572354	0.82[GIH][hapmap];0.89[MKK][hapmap]
rs4924380	0.88[YRI][hapmap]
rs62004771	0.94[ASN][1000 genomes]
rs62004772	0.98[ASN][1000 genomes]
rs67426899	0.94[ASN][1000 genomes]
rs768663	0.82[TSI][hapmap]
rs8028503	0.89[ASN][1000 genomes]
rs8035895	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs937960	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7171939	CASC5	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40021800-40038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:40022400-40023000	Active TSS	A549	lung
3	chr15:40022400-40023200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:40022400-40023200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr15:40022400-40023200	Enhancers	HepG2	liver
6	chr15:40022600-40023200	Enhancers	Fetal Intestine Small	intestine
7	chr15:40022600-40023200	Enhancers	K562	blood

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