Variant report

Variant	rs1879833
Chromosome Location	chr7:47990832-47990833
allele	A/C
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	FOXA2	chr7:47990660-47991584	HepG2	liver:	n/a	n/a
3	STAT3	chr7:47990819-47990894	MCF10A-Er-Src	breast:	n/a	n/a
4	ZEB1	chr7:47990803-47991476	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47988986..47991046-chr7:48004400..48006975,2	MCF-7	breast:

Variant related genes	Relation type
PKD1L1	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1056663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12702401	1.00[CEU][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13309127	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037483	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037485	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242477	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242478	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242479	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686816	0.86[CHB][hapmap]
rs2686817	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2686820	0.86[EUR][1000 genomes]
rs2686821	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2686823	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686825	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686827	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2686830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686834	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686839	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686840	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686841	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686842	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708853	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708858	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708859	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708861	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708865	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708873	0.93[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708877	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708878	0.86[EUR][1000 genomes]
rs2708880	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708881	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708882	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708896	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708897	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708898	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708901	0.81[CEU][hapmap]
rs2708902	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708905	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708910	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708911	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2952720	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3176478	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34016848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35151200	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35536957	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720624	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs57995674	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60107343	0.86[EUR][1000 genomes]
rs6944437	0.82[CEU][hapmap]
rs885337	0.93[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs939904	0.93[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs939905	0.93[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs953572	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953594	0.84[ASN][1000 genomes]
rs9648569	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv8477	chr7:47990804-47990958	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1879833	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr7:47981800-47991200	Weak transcription	A549	lung
12	chr7:47981800-47991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:47982400-47992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:47983600-47993800	Weak transcription	Osteobl	bone
20	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:47983600-48001000	Weak transcription	NHLF	lung
22	chr7:47983800-47993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:47983800-47993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
25	chr7:47984800-47993800	Weak transcription	Esophagus	oesophagus
26	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
28	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
30	chr7:47985400-47993800	Weak transcription	Placenta	Placenta
31	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:47985600-48000600	Weak transcription	Ovary	ovary
33	chr7:47986200-47991200	Weak transcription	Fetal Kidney	kidney
34	chr7:47986200-47991400	Weak transcription	Pancreas	Pancrea
35	chr7:47986400-47991200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr7:47986400-47991200	Enhancers	HUVEC	blood vessel
37	chr7:47986400-47993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:47986400-47993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:47986400-47993800	Weak transcription	HMEC	breast
40	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
41	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
42	chr7:47986600-47993600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:47986800-48001800	Weak transcription	NHEK	skin
45	chr7:47987200-47993200	Weak transcription	Fetal Intestine Small	intestine
46	chr7:47987200-47993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart
48	chr7:47987800-47994000	Weak transcription	Lung	lung
49	chr7:47988200-47993400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:47988600-47993000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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