Variant report

Variant	rs1598859
Chromosome Location	chr4:103506444-103506445
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	chr4:103422373..103425258-chr4:103505770..103508167,2	K562	blood:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs11722146	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11723120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs118882	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs12509403	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs12509517	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs1585215	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1599961	0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1609798	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs17032705	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs170731	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230492	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs230493	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs230495	0.90[JPT][hapmap]
rs230496	0.90[JPT][hapmap]
rs230498	0.93[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]
rs230500	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]
rs230504	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]
rs230505	0.83[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230509	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230511	0.88[CEU][hapmap]
rs230514	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230515	0.86[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs230516	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs230519	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs230520	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]
rs230521	0.91[JPT][hapmap]
rs230525	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs230526	0.83[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230528	0.83[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230529	0.83[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230531	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs230532	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs230533	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230534	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs230535	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs230539	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs230540	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230541	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs230542	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs3755867	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.90[JPT][hapmap]
rs3774936	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774937	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	1.00[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];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3774963	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774964	0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3817685	1.00[JPT][hapmap]
rs3821958	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4235404	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4648011	0.83[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs4648055	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs4648058	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4648068	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs4648133	0.86[CHB][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.81[JPT][hapmap]
rs4698863	0.81[JPT][hapmap]
rs4699030	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs747559	0.91[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9790601	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs980455	0.91[JPT][hapmap];0.83[MEX][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1598859	COL9A2	trans	multi-tissue	Pritchard
rs1598859	MANBA	cis	parietal	SCAN
rs1598859	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
2	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
4	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:103483400-103541600	Weak transcription	K562	blood
6	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
7	chr4:103490800-103519200	Weak transcription	Stomach Mucosa	stomach
8	chr4:103495800-103511800	Strong transcription	Primary B cells from cord blood	blood
9	chr4:103495800-103516400	Weak transcription	NHLF	lung
10	chr4:103496200-103513200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:103496400-103510000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:103497000-103516600	Weak transcription	Brain Substantia Nigra	brain
13	chr4:103497400-103513000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:103497600-103506600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:103497600-103507000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr4:103497800-103509400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr4:103497800-103509400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:103498000-103507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:103498000-103507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:103498000-103508200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr4:103498000-103509000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:103498000-103509600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr4:103498000-103510200	Strong transcription	Adipose Nuclei	Adipose
25	chr4:103498000-103511600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:103498000-103511600	Strong transcription	Dnd41	blood
27	chr4:103498000-103513000	Strong transcription	Liver	Liver
28	chr4:103498000-103513200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:103498200-103511600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:103498200-103513400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:103498200-103513600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:103498600-103507400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:103498800-103520600	Weak transcription	Fetal Brain Female	brain
34	chr4:103499200-103507800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:103500200-103506800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:103500200-103506800	Weak transcription	Aorta	Aorta
37	chr4:103500200-103507000	Weak transcription	Spleen	Spleen
38	chr4:103500200-103511000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:103500200-103511400	Weak transcription	Ovary	ovary
40	chr4:103500200-103515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:103500200-103527600	Weak transcription	Pancreas	Pancrea
42	chr4:103500400-103507000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr4:103500400-103507200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:103500400-103507200	Weak transcription	Thymus	Thymus
45	chr4:103500400-103507800	Weak transcription	Esophagus	oesophagus
46	chr4:103500400-103512000	Weak transcription	A549	lung
47	chr4:103500400-103516400	Weak transcription	Gastric	stomach
48	chr4:103500400-103522600	Weak transcription	Psoas Muscle	Psoas
49	chr4:103500400-103528200	Weak transcription	Right Ventricle	heart
50	chr4:103500800-103517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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