Variant report

Variant	rs2686817
Chromosome Location	chr7:47968927-47968928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1056663	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs12702401	0.81[EUR][1000 genomes]
rs1879833	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1879834	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2242477	0.87[JPT][hapmap]
rs2242478	0.87[JPT][hapmap]
rs2242479	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2686816	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2686820	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686821	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686823	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686825	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686827	0.92[ASN][1000 genomes]
rs2686830	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2686831	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2686832	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2686835	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2686836	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2686838	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2708853	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708861	0.87[JPT][hapmap]
rs2708862	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs2708873	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708878	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708880	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708881	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708894	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2708895	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs2708897	0.80[EUR][1000 genomes]
rs2708903	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2708905	0.87[JPT][hapmap]
rs2708910	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708911	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708913	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3176478	0.87[JPT][hapmap]
rs3176564	0.94[JPT][hapmap]
rs35719200	0.80[ASN][1000 genomes]
rs4720624	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs57995674	0.80[ASN][1000 genomes]
rs60107343	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67565252	0.81[ASN][1000 genomes]
rs6955251	0.83[JPT][hapmap]
rs885337	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939904	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939905	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9648569	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer 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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2686817	UPP1	cis	cerebellum	SCAN
rs2686817	ABCA13	cis	parietal	SCAN
rs2686817	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2686817	PKD1L1	cis	parietal	SCAN
rs2686817	POLM	cis	parietal	SCAN
rs2686817	PKD1L1	cis	cerebellum	SCAN
rs2686817	HUS1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47964000-47970800	Weak transcription	Adipose Nuclei	Adipose
3	chr7:47964800-47970600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:47965000-47972200	Weak transcription	Fetal Stomach	stomach
5	chr7:47965800-47980400	Weak transcription	Aorta	Aorta
6	chr7:47966000-47969600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:47966200-47970800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:47966600-47974000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:47967000-47977400	Weak transcription	Right Ventricle	heart
10	chr7:47967400-47970600	Weak transcription	HSMMtube	muscle
11	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
12	chr7:47967800-47969600	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:47968200-47969600	Enhancers	Primary B cells from cord blood	blood
14	chr7:47968400-47969400	Enhancers	GM12878-XiMat	blood
15	chr7:47968600-47969200	Strong transcription	Left Ventricle	heart
16	chr7:47968600-47969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:47968800-47969200	ZNF genes & repeats	Lung	lung

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