Variant report

Variant	rs2708851
Chromosome Location	chr7:48085802-48085803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48076129..48077793-chr7:48082998..48085969,2	K562	blood:
2	chr7:48080536..48082874-chr7:48084498..48087203,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10247913	0.80[EUR][1000 genomes]
rs10256256	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10276338	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10951942	0.83[TSI][hapmap]
rs11767002	0.81[TSI][hapmap]
rs12535580	0.83[TSI][hapmap]
rs2037482	0.80[EUR][1000 genomes]
rs2348666	0.85[TSI][hapmap]
rs2686783	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2686794	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2686795	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708874	1.00[CEU][hapmap]
rs2708883	0.92[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2708884	0.92[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2708885	0.88[CEU][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2708891	0.84[EUR][1000 genomes]
rs2708901	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2708909	0.96[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6944437	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6978838	0.82[EUR][1000 genomes]
rs6979699	0.82[EUR][1000 genomes]
rs7456745	0.81[CEU][hapmap]
rs7779252	0.81[TSI][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	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
4	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
5	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
6	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
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2708851	LOC100129427	cis	cerebellum	SCAN
rs2708851	UPP1	cis	Muscle Skeletal	GTEx
rs2708851	PKD1L1	cis	parietal	SCAN
rs2708851	ABCA13	cis	parietal	SCAN
rs2708851	PKD1L1	cis	cerebellum	SCAN
rs2708851	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2708851	UPP1	cis	cerebellum	SCAN
rs2708851	HUS1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48080800-48091600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:48081200-48087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:48082000-48086000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:48082600-48086000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:48082800-48087400	Weak transcription	NHEK	skin
6	chr7:48082800-48087600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:48083000-48087600	Weak transcription	HMEC	breast
8	chr7:48083000-48088800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:48083000-48089600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:48083000-48089600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:48083200-48087600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:48084000-48087000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:48084000-48087000	Enhancers	Fetal Thymus	thymus
14	chr7:48084400-48086400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:48084400-48087000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:48084400-48087000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:48084400-48087000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr7:48084600-48086000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:48084600-48086200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:48084600-48086600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:48084600-48086800	Enhancers	Primary T cells fromperipheralblood	blood
22	chr7:48084600-48086800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr7:48084600-48087000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr7:48085000-48087000	Enhancers	Primary T cells from cord blood	blood
25	chr7:48085200-48086200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:48085200-48089600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr7:48085400-48089400	Weak transcription	Thymus	Thymus
28	chr7:48085600-48086800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:48085800-48086000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:48085800-48086200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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