Variant report

Variant	rs13174483
Chromosome Location	chr5:112443320-112443321
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	chr5:112433359..112435186-chr5:112441396..112444395,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10040400	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10067901	0.91[ASN][1000 genomes]
rs10074318	0.89[JPT][hapmap]
rs10478110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241191	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743369	0.92[ASN][1000 genomes]
rs11953203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11960706	0.83[CEU][hapmap]
rs12109548	0.92[CEU][hapmap]
rs12187718	0.88[EUR][1000 genomes]
rs12187866	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12188482	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12517185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12517187	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12523053	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156718	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13179421	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13183472	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs13183638	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]
rs13184187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36041392	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3884576	0.96[ASN][1000 genomes]
rs3922563	0.85[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs3922583	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4078253	0.80[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs4078254	0.80[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs4235793	0.91[ASN][1000 genomes]
rs4262097	0.91[ASN][1000 genomes]
rs4705542	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]
rs4705543	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs4705544	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4705545	0.91[ASN][1000 genomes]
rs4705778	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4705779	0.88[EUR][1000 genomes]
rs4705780	0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4705782	0.80[CEU][hapmap]
rs4705783	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs4705786	0.81[ASN][1000 genomes]
rs4705787	0.91[ASN][1000 genomes]
rs4705788	0.91[ASN][1000 genomes]
rs62374710	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594682	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6594683	0.80[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs6859963	0.89[ASN][1000 genomes]
rs6860460	0.96[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6869399	0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6883605	0.80[CEU][hapmap]
rs7700271	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704382	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7707142	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7731180	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9326877	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9326878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9326879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9885385	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	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
3	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
rs13174483	SRP19	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
10	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
11	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
13	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
15	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
16	chr5:112433800-112443800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:112438000-112444400	Weak transcription	HMEC	breast
21	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
22	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
23	chr5:112438200-112444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
25	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
27	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
28	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
29	chr5:112440000-112443400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112440000-112445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:112440000-112450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:112440200-112445800	Weak transcription	Ovary	ovary
33	chr5:112440200-112446600	Weak transcription	Right Ventricle	heart
34	chr5:112440200-112447800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:112440200-112447800	Weak transcription	Right Atrium	heart
36	chr5:112440200-112448000	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:112440200-112450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:112440200-112450000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:112440200-112450000	Weak transcription	Fetal Stomach	stomach
40	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:112440400-112445800	Weak transcription	Fetal Heart	heart
42	chr5:112441000-112444400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:112441200-112444400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:112441200-112444400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112441400-112444400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:112441400-112444400	Weak transcription	NHEK	skin
47	chr5:112441600-112443600	Enhancers	Left Ventricle	heart
48	chr5:112441600-112444400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:112441600-112447600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:112442400-112446600	Enhancers	Liver	Liver

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