Variant report

Variant	rs4705542
Chromosome Location	chr5:112453010-112453011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10040400	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10067901	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10074318	0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10478110	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11241191	0.97[ASN][1000 genomes]
rs11241192	0.97[ASN][1000 genomes]
rs11241193	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743369	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11953203	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12188482	0.99[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12517185	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12517187	0.97[ASN][1000 genomes]
rs12523053	0.84[ASN][1000 genomes]
rs13156718	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13168126	0.80[CEU][hapmap]
rs13170088	0.84[EUR][1000 genomes]
rs13174483	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs13179421	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13183116	0.80[CEU][hapmap]
rs13183638	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13184187	0.99[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13190424	0.86[EUR][1000 genomes]
rs36041392	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3884576	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922563	0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922583	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]
rs3922585	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs4078252	0.81[CEU][hapmap]
rs4078253	0.82[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4078254	0.82[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235793	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4262097	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705543	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705544	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705545	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705546	0.86[EUR][1000 genomes]
rs4705778	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs4705779	0.80[EUR][1000 genomes]
rs4705780	0.93[ASW][hapmap];0.81[CEU][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705782	0.84[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4705783	0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4705786	0.83[ASN][1000 genomes]
rs4705787	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705788	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705795	0.83[TSI][hapmap]
rs4705797	0.83[TSI][hapmap]
rs62374710	0.97[ASN][1000 genomes]
rs6594682	0.83[ASN][1000 genomes]
rs6594683	0.81[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6859963	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869399	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6883605	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs7700271	0.97[ASN][1000 genomes]
rs7702177	0.81[CEU][hapmap]
rs7704382	0.97[ASN][1000 genomes]
rs7707142	0.92[ASN][1000 genomes]
rs7731180	0.96[ASN][1000 genomes]
rs9326877	0.97[ASN][1000 genomes]
rs9326878	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9326879	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9885385	0.97[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4705542	SRP19	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
2	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
3	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
5	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
8	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
9	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:112448600-112455000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:112448800-112454400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:112448800-112455200	Weak transcription	HUVEC	blood vessel
13	chr5:112449000-112453600	Weak transcription	Right Atrium	heart
14	chr5:112449800-112454200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:112450000-112454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:112450400-112453600	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:112450800-112454600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:112450800-112454600	Weak transcription	Spleen	Spleen
20	chr5:112451000-112453400	Weak transcription	Primary T cells from cord blood	blood
21	chr5:112451000-112453600	Weak transcription	Adipose Nuclei	Adipose
22	chr5:112451000-112454200	Weak transcription	Fetal Brain Male	brain
23	chr5:112451000-112454600	Weak transcription	Lung	lung
24	chr5:112451000-112460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
26	chr5:112451400-112453400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:112451400-112454800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:112451800-112454600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:112451800-112456200	Enhancers	Ovary	ovary
30	chr5:112452000-112454000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr5:112452000-112454800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:112452200-112453400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:112452200-112454400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:112452200-112454600	Enhancers	Fetal Heart	heart
35	chr5:112452200-112455000	Enhancers	Duodenum Mucosa	Duodenum
36	chr5:112452600-112454000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:112452600-112455400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:112452600-112455600	Enhancers	Fetal Lung	lung
39	chr5:112452600-112456800	Enhancers	Fetal Stomach	stomach
40	chr5:112452800-112453800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:112452800-112454000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:112452800-112454000	Enhancers	HMEC	breast
43	chr5:112452800-112454000	Enhancers	NHEK	skin
44	chr5:112452800-112454200	Genic enhancers	Liver	Liver
45	chr5:112452800-112455200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:112452800-112456000	Enhancers	Fetal Muscle Leg	muscle
47	chr5:112452800-112456200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr5:112452800-112456200	Enhancers	Right Ventricle	heart
49	chr5:112452800-112457200	Enhancers	Left Ventricle	heart
50	chr5:112453000-112453200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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