Variant report

Variant	rs3922583
Chromosome Location	chr5:112454991-112454992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10040400	0.83[ASN][1000 genomes]
rs10067901	0.88[ASN][1000 genomes]
rs10074318	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10478110	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11241191	0.93[ASN][1000 genomes]
rs11241192	0.93[ASN][1000 genomes]
rs11241193	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11743369	0.89[ASN][1000 genomes]
rs11953203	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12188482	0.95[ASN][1000 genomes]
rs12517185	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12517187	0.93[ASN][1000 genomes]
rs12523053	0.80[ASN][1000 genomes]
rs13156718	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13174483	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13179421	0.91[ASN][1000 genomes]
rs13183638	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13184187	0.95[ASN][1000 genomes]
rs13190424	0.80[EUR][1000 genomes]
rs1443693	0.96[CEU][hapmap]
rs2044238	0.84[CHB][hapmap]
rs36041392	0.95[ASN][1000 genomes]
rs3884576	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922584	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs3922585	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs4078252	1.00[CEU][hapmap]
rs4078253	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4078254	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4235793	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4262097	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705542	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705543	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705544	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705545	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705546	0.81[EUR][1000 genomes]
rs4705780	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705782	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4705783	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705786	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705787	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705788	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62374710	0.93[ASN][1000 genomes]
rs6594683	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594687	0.96[CEU][hapmap]
rs6859963	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869399	0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6883605	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7700271	0.93[ASN][1000 genomes]
rs7702177	0.96[CEU][hapmap]
rs7704382	0.93[ASN][1000 genomes]
rs7707142	0.88[ASN][1000 genomes]
rs7731180	0.92[ASN][1000 genomes]
rs9326877	0.93[ASN][1000 genomes]
rs9326878	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9326879	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9885385	0.93[ASN][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:71 , 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	chr5:112448600-112455000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:112448800-112455200	Weak transcription	HUVEC	blood vessel
5	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:112451000-112460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
8	chr5:112451800-112456200	Enhancers	Ovary	ovary
9	chr5:112452200-112455000	Enhancers	Duodenum Mucosa	Duodenum
10	chr5:112452600-112455400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112452600-112455600	Enhancers	Fetal Lung	lung
12	chr5:112452600-112456800	Enhancers	Fetal Stomach	stomach
13	chr5:112452800-112455200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:112452800-112456000	Enhancers	Fetal Muscle Leg	muscle
15	chr5:112452800-112456200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:112452800-112456200	Enhancers	Right Ventricle	heart
17	chr5:112452800-112457200	Enhancers	Left Ventricle	heart
18	chr5:112453000-112456200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:112453400-112455200	Enhancers	Brain Anterior Caudate	brain
20	chr5:112453400-112455200	Enhancers	Brain Germinal Matrix	brain
21	chr5:112453400-112456200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:112453600-112455200	Enhancers	Fetal Brain Female	brain
23	chr5:112453600-112455600	Enhancers	Adipose Nuclei	Adipose
24	chr5:112453600-112457200	Enhancers	Right Atrium	heart
25	chr5:112453800-112455000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:112453800-112455000	Weak transcription	Fetal Thymus	thymus
27	chr5:112453800-112455000	Enhancers	Rectal Smooth Muscle	rectum
28	chr5:112453800-112455200	Enhancers	Small Intestine	intestine
29	chr5:112453800-112455400	Enhancers	Stomach Smooth Muscle	stomach
30	chr5:112453800-112456000	Enhancers	HSMMtube	muscle
31	chr5:112453800-112461800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:112454000-112455000	Weak transcription	HMEC	breast
33	chr5:112454000-112455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:112454000-112455200	Weak transcription	NHEK	skin
35	chr5:112454000-112455800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:112454200-112455000	Enhancers	Fetal Brain Male	brain
37	chr5:112454200-112455400	Enhancers	Colon Smooth Muscle	Colon
38	chr5:112454200-112455400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:112454200-112455600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112454200-112456000	Enhancers	Psoas Muscle	Psoas
41	chr5:112454200-112456200	Enhancers	Placenta	Placenta
42	chr5:112454200-112457600	Enhancers	Liver	Liver
43	chr5:112454400-112455400	Enhancers	Fetal Muscle Trunk	muscle
44	chr5:112454400-112456200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:112454400-112456200	Enhancers	Fetal Kidney	kidney
46	chr5:112454400-112456200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr5:112454600-112455000	Flanking Active TSS	Fetal Heart	heart
48	chr5:112454600-112455000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr5:112454600-112455200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:112454600-112455200	Enhancers	Gastric	stomach

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