Variant report

Variant	rs1397529
Chromosome Location	chr4:144392162-144392163
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11725272	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11933502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945261	0.83[EUR][1000 genomes]
rs12512923	0.80[TSI][hapmap]
rs13112412	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13114896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128753	0.80[TSI][hapmap]
rs1397530	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17017801	1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28776014	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28924075	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28925924	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28925926	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28925939	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35152330	0.83[EUR][1000 genomes]
rs3795246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690785	0.80[CEU][hapmap]
rs59727559	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833624	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837464	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7696619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698825	0.88[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9684453	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9685389	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757960	chr4:144348293-145131592	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	esv2759288	chr4:144348293-145131592	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1019980	chr4:144350575-144399936	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2576302	chr4:144390957-144392263	Genic enhancers Strong transcription Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1397529	ANAPC10	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144336400-144392200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:144339400-144394600	Weak transcription	Colonic Mucosa	Colon
3	chr4:144353200-144398600	Weak transcription	Brain Germinal Matrix	brain
4	chr4:144353600-144400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:144360200-144399000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:144363200-144395400	Weak transcription	Spleen	Spleen
7	chr4:144363200-144398600	Weak transcription	Lung	lung
8	chr4:144365600-144398400	Weak transcription	NHLF	lung
9	chr4:144366200-144394400	Weak transcription	Psoas Muscle	Psoas
10	chr4:144373200-144399000	Weak transcription	Fetal Brain Male	brain
11	chr4:144376000-144392800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:144376000-144398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:144376800-144410000	Weak transcription	Pancreas	Pancrea
14	chr4:144377200-144397400	Weak transcription	NHDF-Ad	bronchial
15	chr4:144378600-144393200	Weak transcription	Osteobl	bone
16	chr4:144379400-144399000	Weak transcription	HSMMtube	muscle
17	chr4:144380000-144392200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:144380400-144392400	Strong transcription	Fetal Intestine Large	intestine
19	chr4:144380600-144393600	Strong transcription	Placenta	Placenta
20	chr4:144382800-144396200	Weak transcription	Small Intestine	intestine
21	chr4:144382800-144400600	Weak transcription	Esophagus	oesophagus
22	chr4:144382800-144410200	Weak transcription	Gastric	stomach
23	chr4:144383000-144405800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:144383600-144393200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:144384000-144393400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:144384200-144392600	Weak transcription	Fetal Thymus	thymus
27	chr4:144384200-144400600	Weak transcription	Right Ventricle	heart
28	chr4:144384200-144409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:144384400-144392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:144384400-144400200	Weak transcription	Ovary	ovary
31	chr4:144384800-144397200	Weak transcription	Left Ventricle	heart
32	chr4:144386200-144392200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:144387200-144392200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:144387200-144392400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:144388600-144397400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:144389000-144394600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:144389000-144397400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:144389000-144399200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:144390000-144392600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:144390000-144393000	Strong transcription	Colon Smooth Muscle	Colon
41	chr4:144390000-144394000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:144390400-144397000	Weak transcription	Fetal Stomach	stomach
43	chr4:144390400-144399200	Weak transcription	Fetal Intestine Small	intestine
44	chr4:144390400-144400200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:144390400-144401000	Weak transcription	Aorta	Aorta
46	chr4:144390800-144399600	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:144391000-144392600	Weak transcription	Stomach Mucosa	stomach
48	chr4:144391000-144394800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:144391000-144400000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:144391000-144400000	Weak transcription	Placenta Amnion	Placenta Amnion

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