Variant report

Variant	rs13183638
Chromosome Location	chr5:112450364-112450365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112421011..112422798-chr5:112448533..112450483,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10040400	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10067901	0.90[ASN][1000 genomes]
rs10074318	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10478110	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241191	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241192	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241193	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743369	0.92[ASN][1000 genomes]
rs11953203	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11960706	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12109548	0.92[CEU][hapmap]
rs12187718	0.96[EUR][1000 genomes]
rs12187866	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs12188482	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517185	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12517187	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12523053	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13156718	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179421	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183472	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs13184187	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36041392	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3884576	0.97[ASN][1000 genomes]
rs3922563	0.92[ASW][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.95[ASN][1000 genomes]
rs3922583	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4078253	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs4078254	0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs4235793	0.91[ASN][1000 genomes]
rs4262097	0.94[ASN][1000 genomes]
rs4705542	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]
rs4705543	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705544	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4705545	0.91[ASN][1000 genomes]
rs4705778	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4705779	0.95[EUR][1000 genomes]
rs4705780	0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4705782	0.80[CEU][hapmap];0.86[YRI][hapmap]
rs4705783	0.89[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs4705786	0.82[ASN][1000 genomes]
rs4705787	0.91[ASN][1000 genomes]
rs4705788	0.91[ASN][1000 genomes]
rs62374710	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594682	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6594683	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs6859963	0.90[ASN][1000 genomes]
rs6860460	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs6869399	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6883605	0.80[CEU][hapmap]
rs7700271	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7704382	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7707142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7731180	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9326877	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9885385	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13183638	SRP19	cis	parietal	SCAN
rs13183638	AQPEP	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
6	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
7	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
9	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
12	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
13	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
14	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
15	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
16	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:112442800-112452600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:112448600-112455000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:112448800-112450400	Weak transcription	Left Ventricle	heart
20	chr5:112448800-112454400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:112448800-112455200	Weak transcription	HUVEC	blood vessel
22	chr5:112449000-112452800	Weak transcription	Right Ventricle	heart
23	chr5:112449000-112452800	Weak transcription	HMEC	breast
24	chr5:112449000-112452800	Weak transcription	NHEK	skin
25	chr5:112449000-112453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:112449000-112453600	Weak transcription	Right Atrium	heart
27	chr5:112449200-112452200	Weak transcription	Fetal Heart	heart
28	chr5:112449400-112452600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:112449800-112451600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:112449800-112454200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:112450000-112450800	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr5:112450000-112450800	ZNF genes & repeats	Fetal Stomach	stomach
33	chr5:112450000-112451000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr5:112450000-112451000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:112450000-112451000	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr5:112450000-112451000	ZNF genes & repeats	Lung	lung
37	chr5:112450000-112451000	Strong transcription	Ovary	ovary
38	chr5:112450000-112451400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:112450000-112451800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:112450000-112452200	Strong transcription	Liver	Liver
41	chr5:112450000-112454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:112450200-112450800	ZNF genes & repeats	Spleen	Spleen
44	chr5:112450200-112451000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:112450200-112451000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr5:112450200-112451000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr5:112450200-112452000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:112450200-112452200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:112450200-112452200	Weak transcription	Duodenum Mucosa	Duodenum

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