Variant report

Variant	rs4683502
Chromosome Location	chr3:139248983-139248984
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	chr3:139245782..139250222-chr3:139250781..139254846,5	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1116748	0.86[EUR][1000 genomes]
rs11549984	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12485273	0.85[CEU][hapmap]
rs12489687	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12493507	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1391029	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1391030	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1391031	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1511570	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1511571	0.93[EUR][1000 genomes]
rs17337746	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17397112	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2011770	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3772868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821543	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4270469	0.93[EUR][1000 genomes]
rs4407373	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs55641400	0.93[EUR][1000 genomes]
rs55642746	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55724241	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55780517	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55817881	0.93[EUR][1000 genomes]
rs55834130	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55968289	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55987999	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56034427	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56051054	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56051514	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56058641	0.93[EUR][1000 genomes]
rs56170893	0.93[EUR][1000 genomes]
rs56210757	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56343214	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57459746	0.93[EUR][1000 genomes]
rs73220932	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73220940	0.93[EUR][1000 genomes]
rs73220941	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73220944	0.92[EUR][1000 genomes]
rs893703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893704	0.81[CHD][hapmap]
rs930412	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4683502	RBP1	cis	Liver	GTEx
rs4683502	RBP1	cis	multi-tissue	Pritchard
rs4683502	RBP1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139228800-139253200	Weak transcription	Gastric	stomach
3	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
4	chr3:139234400-139252600	Weak transcription	Lung	lung
5	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
7	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
8	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:139235200-139251400	Weak transcription	Liver	Liver
10	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
12	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
14	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:139239200-139251400	Weak transcription	Placenta	Placenta
16	chr3:139239600-139250000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:139239600-139250000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:139239600-139251400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:139240600-139251000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:139240800-139251800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:139241400-139251200	Strong transcription	Fetal Intestine Small	intestine
22	chr3:139241400-139251200	Strong transcription	Fetal Stomach	stomach
23	chr3:139241400-139253200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:139243800-139251000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:139243800-139252600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:139244000-139249800	Strong transcription	Fetal Intestine Large	intestine
27	chr3:139244400-139251200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:139244400-139251600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:139244800-139250200	Strong transcription	Fetal Lung	lung
30	chr3:139245600-139249200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:139245800-139250200	Weak transcription	Brain Anterior Caudate	brain
32	chr3:139246000-139252000	Weak transcription	Fetal Brain Female	brain
33	chr3:139246400-139250000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:139246600-139252000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:139247000-139249000	Enhancers	Esophagus	oesophagus
36	chr3:139247400-139252600	Weak transcription	Aorta	Aorta
37	chr3:139247600-139250000	Weak transcription	Spleen	Spleen
38	chr3:139247600-139250600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:139247600-139251800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:139247600-139251800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:139247600-139252000	Weak transcription	Left Ventricle	heart
42	chr3:139247800-139249600	Weak transcription	Pancreas	Pancrea
43	chr3:139248000-139251600	Weak transcription	HMEC	breast
44	chr3:139248200-139249000	Enhancers	Ovary	ovary
45	chr3:139248400-139251800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:139248400-139252200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:139248400-139252600	Weak transcription	NHEK	skin
48	chr3:139248600-139250200	Weak transcription	NH-A	brain
49	chr3:139248600-139251600	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:139248600-139252400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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