Variant report

Variant	rs3922585
Chromosome Location	chr5:112455254-112455255
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	chr5:112455253..112458185-chr5:112461323..112464102,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10478110	0.87[JPT][hapmap]
rs11241190	0.88[YRI][hapmap]
rs11749995	0.87[AFR][1000 genomes]
rs11750093	0.88[YRI][hapmap]
rs11953203	0.84[CEU][hapmap]
rs11960706	0.80[CEU][hapmap]
rs12187718	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12187866	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12517185	0.84[JPT][hapmap]
rs13156718	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs13168126	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs13170088	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13173830	0.83[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13183116	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13183472	0.84[CEU][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13190424	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2165930	0.88[CEU][hapmap]
rs2416303	0.81[CEU][hapmap]
rs35334140	0.84[AMR][1000 genomes]
rs3884576	0.84[EUR][1000 genomes]
rs3922563	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs3922583	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs3922584	0.84[CEU][hapmap]
rs4078252	0.84[CEU][hapmap]
rs4078253	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs4078254	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs4235793	0.84[EUR][1000 genomes]
rs4262097	0.85[EUR][1000 genomes]
rs4705542	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs4705543	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4705544	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs4705545	0.83[EUR][1000 genomes]
rs4705546	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705778	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705779	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705780	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs4705782	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705783	0.89[CHB][hapmap]
rs4705787	0.84[EUR][1000 genomes]
rs4705788	0.84[EUR][1000 genomes]
rs4705789	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705795	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs4705797	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs6594683	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs6859963	0.84[EUR][1000 genomes]
rs6883605	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]
rs7702177	0.81[CEU][hapmap]
rs7726679	0.92[CEU][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:112451000-112460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
6	chr5:112451800-112456200	Enhancers	Ovary	ovary
7	chr5:112452600-112455400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112452600-112455600	Enhancers	Fetal Lung	lung
9	chr5:112452600-112456800	Enhancers	Fetal Stomach	stomach
10	chr5:112452800-112456000	Enhancers	Fetal Muscle Leg	muscle
11	chr5:112452800-112456200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:112452800-112456200	Enhancers	Right Ventricle	heart
13	chr5:112452800-112457200	Enhancers	Left Ventricle	heart
14	chr5:112453000-112456200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr5:112453400-112456200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr5:112453600-112455600	Enhancers	Adipose Nuclei	Adipose
17	chr5:112453600-112457200	Enhancers	Right Atrium	heart
18	chr5:112453800-112455400	Enhancers	Stomach Smooth Muscle	stomach
19	chr5:112453800-112456000	Enhancers	HSMMtube	muscle
20	chr5:112453800-112461800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:112454000-112455800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:112454200-112455400	Enhancers	Colon Smooth Muscle	Colon
23	chr5:112454200-112455400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr5:112454200-112455600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:112454200-112456000	Enhancers	Psoas Muscle	Psoas
26	chr5:112454200-112456200	Enhancers	Placenta	Placenta
27	chr5:112454200-112457600	Enhancers	Liver	Liver
28	chr5:112454400-112455400	Enhancers	Fetal Muscle Trunk	muscle
29	chr5:112454400-112456200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:112454400-112456200	Enhancers	Fetal Kidney	kidney
31	chr5:112454400-112456200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr5:112454600-112455400	Enhancers	Esophagus	oesophagus
33	chr5:112454600-112455400	Enhancers	NHLF	lung
34	chr5:112454600-112455600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:112454600-112455600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112454600-112455600	Enhancers	HSMM	muscle
37	chr5:112454600-112455800	Enhancers	Lung	lung
38	chr5:112454600-112456000	Enhancers	Stomach Mucosa	stomach
39	chr5:112454600-112457200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:112454600-112459000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:112454600-112459400	Enhancers	NHDF-Ad	bronchial
42	chr5:112454600-112460600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:112454800-112455400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:112454800-112455400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr5:112454800-112455600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr5:112454800-112455800	Enhancers	Osteobl	bone
47	chr5:112454800-112460400	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:112454800-112460600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:112455000-112455400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:112455000-112455600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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