Variant report

Variant	rs13108722
Chromosome Location	chr4:85634488-85634489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11725121	0.82[EUR][1000 genomes]
rs12500519	0.81[EUR][1000 genomes]
rs12502294	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12502409	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511112	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs13118671	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[EUR][1000 genomes]
rs1484661	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16995920	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17009317	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs17009334	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2218323	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs36036245	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3747680	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816534	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829807	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6838727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6858666	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.81[EUR][1000 genomes]
rs7685537	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7695054	0.80[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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13108722	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85587800-85648400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:85596200-85634600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:85603800-85643800	Weak transcription	Stomach Mucosa	stomach
4	chr4:85604400-85637600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
6	chr4:85605000-85637000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:85607800-85636000	Strong transcription	Fetal Lung	lung
8	chr4:85611600-85636600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr4:85612600-85639600	Weak transcription	Fetal Heart	heart
10	chr4:85613400-85643000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:85613400-85646200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:85613400-85646600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:85613400-85649400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:85613600-85650200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:85616800-85646600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:85617000-85641800	Weak transcription	Psoas Muscle	Psoas
18	chr4:85619200-85636800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
20	chr4:85619400-85636600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:85619400-85639000	Strong transcription	Adipose Nuclei	Adipose
22	chr4:85619400-85646400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:85619600-85638400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:85619600-85646400	Strong transcription	Liver	Liver
25	chr4:85620000-85636000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:85620200-85635800	Strong transcription	Brain Germinal Matrix	brain
27	chr4:85620200-85640000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:85620200-85648000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:85620800-85663400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:85621200-85635800	Strong transcription	HSMM	muscle
31	chr4:85621600-85636600	Strong transcription	Fetal Intestine Large	intestine
32	chr4:85621600-85636800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:85622000-85635600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr4:85623200-85635600	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr4:85623200-85640400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:85625000-85646600	Strong transcription	Placenta	Placenta
37	chr4:85625200-85641600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:85625600-85636400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:85626800-85641600	Weak transcription	NHEK	skin
40	chr4:85626800-85641800	Weak transcription	HMEC	breast
41	chr4:85627800-85646800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:85628800-85641600	Weak transcription	Aorta	Aorta
43	chr4:85628800-85641600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:85628800-85641600	Weak transcription	Spleen	Spleen
45	chr4:85628800-85642000	Weak transcription	Gastric	stomach
46	chr4:85629200-85662400	Weak transcription	Colonic Mucosa	Colon
47	chr4:85630000-85638600	Weak transcription	Ovary	ovary
48	chr4:85630000-85641200	Weak transcription	NHLF	lung
49	chr4:85630000-85641400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:85630000-85641600	Weak transcription	Pancreas	Pancrea

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