Variant report

Variant	rs230520
Chromosome Location	chr4:103465612-103465613
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	chr4:103421329..103424416-chr4:103463200..103466057,3	K562	blood:
2	chr4:103420096..103422829-chr4:103464276..103466057,2	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs12509517	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1585215	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs1599961	0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs170731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs230500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs230504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs230505	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs230526	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230528	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230529	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs230532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs230539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230540	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs230542	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs3774963	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774964	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4648055	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.83[CEU][hapmap]
rs4699030	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs747559	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs9790601	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs980455	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription 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	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs230520	MANBA	cis	parietal	SCAN
rs230520	MANBA	cis	multi-tissue	Pritchard
rs230520	CISD2	cis	parietal	SCAN
rs230520	BANK1	cis	parietal	SCAN
rs230520	ADH7	cis	cerebellum	SCAN
rs230520	COL9A2	trans	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
2	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
3	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
6	chr4:103440200-103488200	Weak transcription	Gastric	stomach
7	chr4:103441400-103469400	Weak transcription	Ovary	ovary
8	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
9	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:103443200-103496000	Weak transcription	A549	lung
11	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
13	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:103446200-103466000	Weak transcription	Lung	lung
16	chr4:103446200-103469200	Weak transcription	Pancreas	Pancrea
17	chr4:103446200-103469800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:103446600-103466200	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:103447200-103474000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:103449000-103467000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:103449400-103467000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:103449600-103467800	Weak transcription	Fetal Kidney	kidney
23	chr4:103455400-103474600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:103456400-103472200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:103456400-103473400	Weak transcription	Fetal Lung	lung
26	chr4:103456800-103475600	Weak transcription	Brain Anterior Caudate	brain
27	chr4:103457200-103467000	Strong transcription	Primary B cells from cord blood	blood
28	chr4:103457200-103474800	Weak transcription	NHLF	lung
29	chr4:103457800-103471600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:103458000-103466000	Weak transcription	NH-A	brain
31	chr4:103458000-103475200	Weak transcription	NHDF-Ad	bronchial
32	chr4:103458800-103467800	Weak transcription	Stomach Mucosa	stomach
33	chr4:103458800-103473600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:103459000-103469400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:103460400-103466200	Weak transcription	Fetal Intestine Small	intestine
36	chr4:103461200-103469400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:103461200-103469400	Weak transcription	Fetal Stomach	stomach
38	chr4:103461200-103474800	Weak transcription	Osteobl	bone
39	chr4:103461200-103487800	Weak transcription	Colonic Mucosa	Colon
40	chr4:103461200-103490400	Weak transcription	Dnd41	blood
41	chr4:103461400-103466400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:103461400-103469400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:103461600-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:103462600-103466400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:103462600-103467000	Strong transcription	Adipose Nuclei	Adipose
47	chr4:103462800-103469600	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:103463200-103465800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:103463200-103466000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:103463200-103466000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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