Variant report

Variant	rs2686840
Chromosome Location	chr7:48009761-48009762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:47884198..47887290-chr7:48007408..48010423,4	MCF-7	breast:
2	chr7:47992039..47994251-chr7:48008798..48010394,2	MCF-7	breast:
3	chr7:48007920..48009959-chr7:48011968..48013764,2	MCF-7	breast:
4	chr7:48008512..48011400-chr7:48014003..48016517,2	MCF-7	breast:
5	chr7:48008475..48011442-chr7:48016740..48019056,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1056663	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12702401	0.86[AMR][1000 genomes]
rs13309127	0.86[AMR][1000 genomes]
rs1879833	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879834	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2037483	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2037485	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2242477	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2242478	0.83[AMR][1000 genomes]
rs2242479	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2686830	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686831	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686832	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686833	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686834	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686835	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2686836	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686838	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2686839	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2686841	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2686842	0.83[AMR][1000 genomes]
rs2708858	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2708859	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2708861	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2708862	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708865	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708873	0.81[AMR][1000 genomes]
rs2708877	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708882	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708894	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2708895	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2708896	0.82[AMR][1000 genomes]
rs2708897	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2708898	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2708902	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708903	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2952720	0.86[AMR][1000 genomes]
rs3176564	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34016848	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35151200	0.82[AMR][1000 genomes]
rs35536957	0.84[AMR][1000 genomes]
rs953572	0.87[AMR][1000 genomes];0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2686840	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
2	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
3	chr7:48000200-48016600	Strong transcription	Liver	Liver
4	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:48000400-48010000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:48000400-48011200	Strong transcription	Colon Smooth Muscle	Colon
7	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:48000600-48010000	Strong transcription	NHDF-Ad	bronchial
14	chr7:48000600-48010200	Strong transcription	Fetal Muscle Leg	muscle
15	chr7:48000600-48011200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:48000600-48011400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:48000600-48015800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:48000600-48017600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:48001000-48009800	Strong transcription	Fetal Intestine Small	intestine
20	chr7:48001600-48017600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:48002000-48018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:48004000-48011400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:48005800-48013800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:48007000-48011000	Weak transcription	Brain Germinal Matrix	brain
25	chr7:48007200-48010800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:48007200-48010800	Weak transcription	Pancreas	Pancrea
27	chr7:48007200-48010800	Weak transcription	Spleen	Spleen
28	chr7:48007200-48012400	Weak transcription	Gastric	stomach
29	chr7:48007200-48013000	Weak transcription	Right Ventricle	heart
30	chr7:48007200-48013600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:48007200-48013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:48007400-48012600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:48007400-48018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr7:48007600-48010200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:48007600-48011000	Weak transcription	Aorta	Aorta
36	chr7:48007600-48012600	Weak transcription	Small Intestine	intestine
37	chr7:48007600-48013000	Weak transcription	Stomach Mucosa	stomach
38	chr7:48007600-48013800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:48007800-48010000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:48007800-48010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:48007800-48011000	Weak transcription	Esophagus	oesophagus
42	chr7:48007800-48011000	Weak transcription	Fetal Brain Female	brain
43	chr7:48007800-48011000	Weak transcription	HSMMtube	muscle
44	chr7:48007800-48011200	Weak transcription	Ovary	ovary
45	chr7:48007800-48012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:48007800-48012200	Weak transcription	HepG2	liver
47	chr7:48007800-48012600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:48007800-48013400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:48007800-48013800	Weak transcription	Dnd41	blood
50	chr7:48007800-48015400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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