Variant report

Variant	rs35536957
Chromosome Location	chr7:47990222-47990223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:47990171-47991966	MCF-7	breast:	n/a	chr7:47991804-47991820 chr7:47991802-47991823 chr7:47991701-47991710 chr7:47991804-47991820
2	STAT3	chr7:47990119-47990598	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47988986..47991046-chr7:48004400..48006975,2	MCF-7	breast:
2	chr7:47984965..47986938-chr7:47988162..47990314,2	K562	blood:

Variant related genes	Relation type
PKD1L1	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1056663	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12702401	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13309127	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879833	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879834	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037483	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2037485	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242477	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242478	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242479	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686820	0.83[EUR][1000 genomes]
rs2686821	0.83[EUR][1000 genomes]
rs2686823	0.83[EUR][1000 genomes]
rs2686825	0.83[EUR][1000 genomes]
rs2686830	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686831	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686832	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686833	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686834	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2686835	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2686836	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2686838	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2686839	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686840	0.84[AMR][1000 genomes]
rs2686841	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2686842	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708853	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708858	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708859	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708861	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708862	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708865	0.87[AMR][1000 genomes]
rs2708873	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708875	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2708877	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708878	0.83[EUR][1000 genomes]
rs2708880	0.83[EUR][1000 genomes]
rs2708881	0.83[EUR][1000 genomes]
rs2708882	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708894	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708895	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708896	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2708897	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708898	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708902	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708903	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708905	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708910	0.83[EUR][1000 genomes]
rs2708911	0.83[EUR][1000 genomes]
rs2952720	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3176478	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3176564	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34016848	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35151200	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57995674	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60107343	0.83[EUR][1000 genomes]
rs885337	0.82[EUR][1000 genomes]
rs939904	0.82[EUR][1000 genomes]
rs939905	0.82[EUR][1000 genomes]
rs953572	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs953594	0.83[AMR][1000 genomes];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35536957	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
3	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
6	chr7:47978600-47992600	Weak transcription	Primary B cells from cord blood	blood
7	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:47980800-47993000	Weak transcription	Fetal Stomach	stomach
9	chr7:47981200-47991400	Weak transcription	Colonic Mucosa	Colon
10	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
11	chr7:47981800-47990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:47981800-47990800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:47981800-47991200	Weak transcription	A549	lung
14	chr7:47981800-47991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:47982400-47992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:47983600-47993800	Weak transcription	Osteobl	bone
22	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:47983600-48001000	Weak transcription	NHLF	lung
24	chr7:47983800-47993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:47983800-47993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
27	chr7:47984800-47993800	Weak transcription	Esophagus	oesophagus
28	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
30	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
32	chr7:47985400-47993800	Weak transcription	Placenta	Placenta
33	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:47985600-48000600	Weak transcription	Ovary	ovary
35	chr7:47986200-47991200	Weak transcription	Fetal Kidney	kidney
36	chr7:47986200-47991400	Weak transcription	Pancreas	Pancrea
37	chr7:47986400-47991200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:47986400-47991200	Enhancers	HUVEC	blood vessel
39	chr7:47986400-47993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:47986400-47993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:47986400-47993800	Weak transcription	HMEC	breast
42	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
43	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
44	chr7:47986600-47993600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:47986800-47990400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:47986800-48001800	Weak transcription	NHEK	skin
48	chr7:47987200-47993200	Weak transcription	Fetal Intestine Small	intestine
49	chr7:47987200-47993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart

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