Variant report

Variant	rs6883605
Chromosome Location	chr5:112460633-112460634
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	chr5:112459886..112461931-chr5:112462862..112464863,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11749995	0.89[AFR][1000 genomes]
rs11953203	0.84[CEU][hapmap]
rs11960706	0.81[CEU][hapmap]
rs12187718	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12187866	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13156718	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs13168126	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13170088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13173830	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13174483	0.80[CEU][hapmap]
rs13183116	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13183472	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13183638	0.80[CEU][hapmap]
rs13190424	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165930	0.88[CEU][hapmap]
rs2416303	0.81[CEU][hapmap]
rs35334140	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3884576	0.83[EUR][1000 genomes]
rs3922563	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3922583	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs3922584	0.81[CEU][hapmap]
rs3922585	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078252	0.81[CEU][hapmap]
rs4078253	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs4078254	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs4235793	0.86[EUR][1000 genomes]
rs4262097	0.87[EUR][1000 genomes]
rs4705542	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4705543	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4705544	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4705545	0.85[EUR][1000 genomes]
rs4705546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705778	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705779	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705780	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs4705782	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705787	0.86[EUR][1000 genomes]
rs4705788	0.86[EUR][1000 genomes]
rs4705789	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705795	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4705797	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs6594683	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs6859963	0.86[EUR][1000 genomes]
rs7726679	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9326879	0.80[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
3	chr5:112453800-112461800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:112455000-112462200	Enhancers	Fetal Heart	heart
5	chr5:112455400-112461400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:112455400-112461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:112456600-112467200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:112457400-112462000	Enhancers	Adipose Nuclei	Adipose
9	chr5:112458400-112474200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:112458600-112474000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:112458600-112477000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:112458800-112476600	Weak transcription	NHEK	skin
13	chr5:112459200-112460800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112459200-112461400	Enhancers	Right Ventricle	heart
15	chr5:112459200-112462000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:112459400-112460800	Enhancers	Brain Germinal Matrix	brain
17	chr5:112459400-112460800	Enhancers	Fetal Kidney	kidney
18	chr5:112459400-112461600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:112459400-112461600	Enhancers	Fetal Brain Female	brain
20	chr5:112459400-112468400	Weak transcription	NHDF-Ad	bronchial
21	chr5:112459600-112461800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:112459600-112462200	Enhancers	Liver	Liver
23	chr5:112459600-112462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:112459800-112462600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:112460000-112460800	Enhancers	Fetal Brain Male	brain
26	chr5:112460000-112461200	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr5:112460000-112461600	Enhancers	Fetal Lung	lung
28	chr5:112460000-112461800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:112460200-112461000	Enhancers	Right Atrium	heart
30	chr5:112460200-112461400	Enhancers	Left Ventricle	heart
31	chr5:112460200-112462000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:112460400-112460800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:112460400-112460800	Enhancers	Psoas Muscle	Psoas
34	chr5:112460400-112461000	Enhancers	Brain Hippocampus Middle	brain
35	chr5:112460400-112461400	Enhancers	Ovary	ovary
36	chr5:112460600-112460800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:112460600-112460800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr5:112460600-112460800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:112460600-112460800	Enhancers	Pancreas	Pancrea
40	chr5:112460600-112460800	Enhancers	Osteobl	bone
41	chr5:112460600-112461400	Enhancers	Fetal Muscle Leg	muscle
42	chr5:112460600-112462400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr5:112460600-112462600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:112460600-112463600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:112460600-112465000	Weak transcription	Stomach Smooth Muscle	stomach

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