Variant report

Variant	rs10031136
Chromosome Location	chr4:77407344-77407345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10002170	0.93[AFR][1000 genomes]
rs11723732	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13146564	0.90[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13152154	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1398017	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1511817	0.82[CEU][hapmap]
rs1849215	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1949137	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2136854	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4241593	0.89[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4475168	0.93[AFR][1000 genomes]
rs4859445	0.82[CEU][hapmap]
rs4859673	0.85[CEU][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859674	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859688	0.80[GIH][hapmap]
rs62300863	0.90[EUR][1000 genomes]
rs62300882	0.82[EUR][1000 genomes]
rs6532414	0.90[AFR][1000 genomes]
rs6532416	0.89[ASN][1000 genomes]
rs6532417	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839100	0.82[EUR][1000 genomes]
rs6843293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][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	esv2757941	chr4:77264596-77417457	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759262	chr4:77264596-77455405	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757069	chr4:77392092-77455405	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10031136	CCDC158	cis	parietal	SCAN
rs10031136	FGF5	cis	cerebellum	SCAN
rs10031136	ART3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77405400-77407600	Enhancers	Liver	Liver
2	chr4:77405600-77408200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr4:77405600-77408200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:77405600-77411200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:77405800-77407800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:77405800-77408000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr4:77405800-77408000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:77405800-77408000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:77405800-77408000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:77405800-77408000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:77405800-77408200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:77405800-77408400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:77406000-77407400	Enhancers	Fetal Heart	heart
14	chr4:77406000-77407800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:77406000-77408000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:77406000-77409400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:77406400-77407800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:77406600-77407400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:77406600-77407400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:77406600-77407400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:77406600-77407400	Enhancers	HMEC	breast
22	chr4:77406600-77407600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:77406600-77407600	Weak transcription	Stomach Mucosa	stomach
24	chr4:77406600-77408400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:77406600-77408800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:77406600-77408800	Enhancers	Fetal Intestine Small	intestine
27	chr4:77406800-77417200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:77407000-77410000	Weak transcription	NH-A	brain
29	chr4:77407000-77416600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:77407000-77419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:77407200-77408400	Enhancers	Duodenum Mucosa	Duodenum
32	chr4:77407200-77409400	Enhancers	Fetal Intestine Large	intestine

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