Variant report

Variant	rs4705778
Chromosome Location	chr5:112448907-112448908
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	chr5:112421011..112422798-chr5:112448533..112450483,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10040400	0.93[EUR][1000 genomes]
rs10478110	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11241191	0.86[EUR][1000 genomes]
rs11241192	0.88[EUR][1000 genomes]
rs11241193	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs11953203	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11960706	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12109548	0.85[CEU][hapmap]
rs12187718	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12187866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12188482	0.95[EUR][1000 genomes]
rs12517185	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12517187	0.88[EUR][1000 genomes]
rs12523053	0.84[EUR][1000 genomes]
rs13156718	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs13168126	0.84[CEU][hapmap]
rs13170088	0.89[ASN][1000 genomes]
rs13173830	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13174483	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs13179421	0.95[EUR][1000 genomes]
rs13183116	0.84[CEU][hapmap]
rs13183472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183638	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs13184187	0.95[EUR][1000 genomes]
rs13190424	0.88[ASN][1000 genomes]
rs36041392	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3922585	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705542	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs4705543	0.81[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4705546	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705779	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705782	0.88[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705795	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs4705797	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs62374710	0.88[EUR][1000 genomes]
rs6594682	0.85[EUR][1000 genomes]
rs6860460	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs6883605	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7700271	0.88[EUR][1000 genomes]
rs7704382	0.87[EUR][1000 genomes]
rs7707142	0.88[EUR][1000 genomes]
rs7726679	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs7731180	0.88[EUR][1000 genomes]
rs9326877	0.87[EUR][1000 genomes]
rs9326878	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9326879	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs9885385	0.88[EUR][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
rs4705778	SRP19	cis	parietal	SCAN

Chromatin state (count:48 , 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	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
5	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
7	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
8	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
10	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
11	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
14	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
15	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
16	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
18	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
19	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
20	chr5:112440000-112450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:112440200-112450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:112440200-112450000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:112440200-112450000	Weak transcription	Fetal Stomach	stomach
24	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:112442800-112452600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:112444800-112450000	Weak transcription	Lung	lung
27	chr5:112446400-112450200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:112446600-112449000	Enhancers	Right Ventricle	heart
29	chr5:112446600-112450000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:112446600-112450000	Weak transcription	Liver	Liver
31	chr5:112447200-112450000	Weak transcription	Ovary	ovary
32	chr5:112447800-112449000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:112447800-112449000	Enhancers	Right Atrium	heart
34	chr5:112447800-112449200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:112448000-112449000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:112448000-112449000	Enhancers	Fetal Muscle Leg	muscle
37	chr5:112448000-112449000	Genic enhancers	NHEK	skin
38	chr5:112448200-112449800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:112448600-112449000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:112448600-112449000	Weak transcription	Fetal Heart	heart
41	chr5:112448600-112449000	Enhancers	HMEC	breast
42	chr5:112448600-112449800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:112448600-112450000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:112448600-112455000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:112448800-112449000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:112448800-112450400	Weak transcription	Left Ventricle	heart
47	chr5:112448800-112454400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:112448800-112455200	Weak transcription	HUVEC	blood vessel

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