Variant report

Variant	rs2708911
Chromosome Location	chr7:47979209-47979210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:47969215..47970868-chr7:47978587..47981152,2	K562	blood:
2	chr7:47978394..47981153-chr7:48011977..48014017,2	K562	blood:
3	chr7:47977182..47979989-chr7:47980924..47982675,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1056663	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs12702401	0.91[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879833	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1879834	0.93[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2037483	0.85[EUR][1000 genomes]
rs2037485	0.85[EUR][1000 genomes]
rs2242477	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2242478	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2242479	0.88[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2686816	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2686817	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]
rs2686820	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686823	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686827	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686830	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686831	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686832	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686833	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686834	0.85[EUR][1000 genomes]
rs2686835	0.93[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686836	0.93[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2686838	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686839	0.84[EUR][1000 genomes]
rs2686841	0.83[EUR][1000 genomes]
rs2708853	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708858	0.81[EUR][1000 genomes]
rs2708859	0.81[EUR][1000 genomes]
rs2708861	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2708862	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2708873	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.81[CEU][hapmap]
rs2708877	0.85[EUR][1000 genomes]
rs2708878	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708880	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708881	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708882	0.85[EUR][1000 genomes]
rs2708894	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708895	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708896	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2708897	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708898	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708901	0.80[CEU][hapmap]
rs2708902	0.82[EUR][1000 genomes]
rs2708903	0.93[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2708905	0.89[CEU][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs2708910	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708913	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176478	0.87[JPT][hapmap]
rs3176564	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs34016848	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35536957	0.83[EUR][1000 genomes]
rs4720624	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs57995674	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60107343	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67565252	0.80[ASN][1000 genomes]
rs6955251	0.83[JPT][hapmap]
rs885337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939904	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953572	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9648569	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]

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
rs2708911	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2708911	POLM	cis	parietal	SCAN
rs2708911	UPP1	cis	cerebellum	SCAN
rs2708911	PKD1L1	cis	parietal	SCAN
rs2708911	PKD1L1	cis	cerebellum	SCAN
rs2708911	HUS1	cis	cerebellum	SCAN
rs2708911	ABCA13	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47965800-47980400	Weak transcription	Aorta	Aorta
3	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
4	chr7:47972600-47980400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:47972800-47979600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:47974000-47979600	Weak transcription	Adipose Nuclei	Adipose
7	chr7:47974800-47979400	Weak transcription	Lung	lung
8	chr7:47974800-47979400	Weak transcription	HSMMtube	muscle
9	chr7:47974800-47980200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:47975800-47982400	Enhancers	Fetal Heart	heart
11	chr7:47976000-47979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:47976000-47986000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:47976600-47980800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:47976800-47979600	Weak transcription	HSMM	muscle
15	chr7:47977000-47979600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr7:47977200-47979800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:47977200-47980000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:47977200-47980400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:47977200-47980400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:47977200-47980800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:47977200-47980800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:47977400-47981800	Enhancers	Right Ventricle	heart
23	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:47977600-47979400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:47977600-47979800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:47977600-47980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:47978200-47980200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:47978400-47979400	Weak transcription	Colonic Mucosa	Colon
29	chr7:47978400-47979400	Enhancers	GM12878-XiMat	blood
30	chr7:47978400-47983600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
33	chr7:47978600-47982000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:47978600-47992600	Weak transcription	Primary B cells from cord blood	blood
35	chr7:47978800-47980400	Weak transcription	A549	lung
36	chr7:47978800-47981200	Enhancers	Duodenum Mucosa	Duodenum
37	chr7:47978800-47981400	Enhancers	Spleen	Spleen
38	chr7:47978800-47983600	Enhancers	NHLF	lung
39	chr7:47979000-47979800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr7:47979000-47981000	Enhancers	Fetal Intestine Small	intestine
41	chr7:47979000-47981800	Enhancers	Right Atrium	heart
42	chr7:47979000-47982400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr7:47979200-47979600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr7:47979200-47980400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:47979200-47981000	Enhancers	Fetal Intestine Large	intestine
46	chr7:47979200-47981200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr7:47979200-47981800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr7:47979200-47982000	Enhancers	Left Ventricle	heart

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