Variant report

Variant	rs6836616
Chromosome Location	chr4:15482668-15482669
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15481667..15484454-chr4:15772642..15775403,2	MCF-7	breast:
2	chr4:15480883..15483744-chr4:15651050..15653259,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10004540	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10032808	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10516286	1.00[CEU][hapmap]
rs11942186	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11942959	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13353624	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468737	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1861049	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080176	0.83[JPT][hapmap]
rs2080177	0.83[JPT][hapmap]
rs2192359	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192360	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192361	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192362	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28405315	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28448602	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28465445	0.95[ASN][1000 genomes]
rs28517424	0.81[ASN][1000 genomes]
rs28697056	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3822297	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4140933	0.83[JPT][hapmap]
rs4698107	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698108	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698112	0.83[JPT][hapmap]
rs4698381	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4698383	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698384	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60487386	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61170754	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6810461	0.83[JPT][hapmap]
rs6814988	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6837765	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7656974	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7661435	0.81[ASN][1000 genomes]
rs971490	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9998686	0.83[JPT][hapmap]
rs9998722	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6836616	LOC285550	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481200-15485200	Weak transcription	Right Ventricle	heart
2	chr4:15481400-15486200	Weak transcription	Spleen	Spleen
3	chr4:15481600-15484000	Weak transcription	Aorta	Aorta
4	chr4:15481600-15484200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:15481600-15484400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:15481600-15484400	Weak transcription	Placenta	Placenta
7	chr4:15481600-15484400	Weak transcription	K562	blood
8	chr4:15481600-15484600	Weak transcription	Right Atrium	heart
9	chr4:15481600-15488000	Weak transcription	HSMMtube	muscle
10	chr4:15481600-15490200	Weak transcription	Esophagus	oesophagus
11	chr4:15481600-15498600	Weak transcription	Liver	Liver
12	chr4:15481600-15519000	Weak transcription	Gastric	stomach
13	chr4:15481800-15483200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:15481800-15483200	Weak transcription	Fetal Kidney	kidney
15	chr4:15481800-15484000	Weak transcription	Ovary	ovary
16	chr4:15481800-15488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:15482000-15482800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:15482000-15482800	Enhancers	NH-A	brain
19	chr4:15482000-15483200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:15482000-15484000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:15482000-15484200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:15482000-15485400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:15482000-15486400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:15482000-15486600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:15482000-15487000	Weak transcription	HSMM	muscle
26	chr4:15482000-15487600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:15482000-15489600	Weak transcription	Brain Substantia Nigra	brain
28	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:15482200-15482800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:15482200-15484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:15482200-15484600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:15482200-15484600	Weak transcription	NHEK	skin
34	chr4:15482200-15485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:15482200-15485000	Strong transcription	Fetal Intestine Small	intestine
36	chr4:15482200-15486200	Strong transcription	Fetal Stomach	stomach
37	chr4:15482200-15486400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:15482200-15486600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:15482200-15487600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:15482200-15490400	Weak transcription	A549	lung
41	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:15482400-15482800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:15482400-15483000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:15482400-15483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:15482400-15483400	Strong transcription	Lung	lung
46	chr4:15482400-15483400	Weak transcription	NHDF-Ad	bronchial
47	chr4:15482400-15483600	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:15482400-15484600	Weak transcription	Fetal Brain Female	brain
49	chr4:15482400-15484800	Weak transcription	Fetal Lung	lung
50	chr4:15482400-15485000	Strong transcription	Fetal Intestine Large	intestine

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