Variant report

Variant	rs230500
Chromosome Location	chr4:103491724-103491725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103479897..103481951-chr4:103489353..103491766,3	K562	blood:
2	chr4:103489104..103492778-chr4:103495068..103498574,4	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11723120	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs118882	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs12509403	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs12509517	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	1.00[JPT][hapmap];0.91[MEX][hapmap]
rs1585215	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1599961	1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs17032705	1.00[JPT][hapmap];0.91[MEX][hapmap]
rs170731	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230493	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs230505	0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230509	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230511	0.88[CEU][hapmap]
rs230514	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs230520	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]
rs230521	1.00[JPT][hapmap]
rs230525	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs230526	0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230528	0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230529	0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs230532	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs230533	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230534	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230535	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs230539	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230540	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230541	0.84[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs230542	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs3755867	0.87[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3774963	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774964	0.84[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs4235404	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4648055	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs4648133	0.81[CHB][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4699030	0.84[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs747559	1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9790601	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs980455	1.00[JPT][hapmap];0.83[MEX][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs230500	COL9A2	trans	multi-tissue	Pritchard
rs230500	MANBA	cis	multi-tissue	Pritchard
rs230500	MANBA	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103443200-103496000	Weak transcription	A549	lung
2	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
5	chr4:103467000-103495600	Weak transcription	HepG2	liver
6	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
7	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
8	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
9	chr4:103473600-103498000	Weak transcription	Aorta	Aorta
10	chr4:103475000-103496600	Weak transcription	HUVEC	blood vessel
11	chr4:103475200-103496400	Weak transcription	Hela-S3	cervix
12	chr4:103476000-103498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:103476400-103498000	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:103476400-103498200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:103478600-103498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:103479200-103497800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:103482200-103495400	Weak transcription	Fetal Thymus	thymus
19	chr4:103482200-103498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:103482200-103498800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:103482400-103498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:103482800-103496600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:103482800-103497800	Weak transcription	Fetal Intestine Large	intestine
24	chr4:103482800-103498000	Weak transcription	Fetal Intestine Small	intestine
25	chr4:103482800-103498200	Weak transcription	Brain Anterior Caudate	brain
26	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
27	chr4:103483200-103498000	Weak transcription	Right Ventricle	heart
28	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
29	chr4:103483400-103497800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:103483400-103498000	Weak transcription	Pancreas	Pancrea
31	chr4:103483400-103498200	Weak transcription	Left Ventricle	heart
32	chr4:103483400-103498200	Weak transcription	Ovary	ovary
33	chr4:103483400-103541600	Weak transcription	K562	blood
34	chr4:103484000-103498000	Weak transcription	Spleen	Spleen
35	chr4:103486000-103498000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:103486000-103498000	Weak transcription	Liver	Liver
37	chr4:103486000-103498000	Weak transcription	HSMMtube	muscle
38	chr4:103486200-103495400	Weak transcription	NHLF	lung
39	chr4:103486200-103496200	Weak transcription	NH-A	brain
40	chr4:103486400-103497800	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:103486600-103493600	Weak transcription	Thymus	Thymus
42	chr4:103486600-103498200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:103487200-103491800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:103487600-103491800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:103487600-103493000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:103487800-103491800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
48	chr4:103488400-103498000	Weak transcription	Colonic Mucosa	Colon
49	chr4:103488400-103498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:103488600-103492000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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