Variant report

Variant	rs2085292
Chromosome Location	chr4:48914936-48914937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48908480..48910327-chr4:48912176..48914944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10517231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727343	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs11729065	0.81[ASN][1000 genomes]
rs11733534	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.93[YRI][hapmap]
rs11734191	0.83[ASN][1000 genomes]
rs11737706	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504699	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12512637	0.91[JPT][hapmap]
rs13142540	0.89[YRI][hapmap]
rs13146034	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13149083	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.96[YRI][hapmap]
rs13152270	0.84[ASN][1000 genomes]
rs1455940	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1463365	0.92[ASN][1000 genomes]
rs1554256	0.85[MEX][hapmap];0.96[YRI][hapmap]
rs2247481	0.81[LWK][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap]
rs2289065	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2290516	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572345	0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs2572350	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2605267	0.92[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs2712156	0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs2712158	0.84[CHD][hapmap]
rs34730980	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3761729	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs4694906	0.91[JPT][hapmap]
rs4695407	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs6447666	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs6447670	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654032	0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs7660206	0.85[MEX][hapmap];0.85[YRI][hapmap]
rs7665209	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7672280	0.87[EUR][1000 genomes]
rs7685360	0.85[ASN][1000 genomes]
rs7687992	0.83[ASN][1000 genomes]
rs9291326	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs9637562	0.81[ASN][1000 genomes]
rs9997920	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2085292	SLC10A4	cis	lung	GTEx
rs2085292	OCIAD2	cis	lymphoblastoid	seeQTL
rs2085292	OCIAD2	cis	cerebellum	SCAN
rs2085292	TEC	cis	parietal	SCAN
rs2085292	MGC45416	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48909200-48916200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:48909400-48917200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:48911600-48915400	Weak transcription	NHLF	lung
4	chr4:48911800-48915200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:48911800-48916200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:48912200-48915000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:48912200-48915200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:48912200-48915400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:48913000-48916800	Weak transcription	Stomach Mucosa	stomach
10	chr4:48913600-48917200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:48914400-48917200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:48914400-48917400	Enhancers	NHEK	skin
13	chr4:48914600-48915400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:48914600-48915800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:48914600-48915800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:48914600-48915800	Enhancers	Esophagus	oesophagus
17	chr4:48914600-48915800	Enhancers	Stomach Smooth Muscle	stomach
18	chr4:48914600-48916800	Enhancers	NHDF-Ad	bronchial
19	chr4:48914600-48917000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:48914600-48917000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:48914600-48917000	Enhancers	HMEC	breast
22	chr4:48914600-48917000	Enhancers	HUVEC	blood vessel
23	chr4:48914600-48917000	Enhancers	NH-A	brain
24	chr4:48914800-48915800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:48914800-48915800	Enhancers	HSMM	muscle
26	chr4:48914800-48916000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:48914800-48916800	Enhancers	Osteobl	bone

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