Variant report

Variant	rs1599961
Chromosome Location	chr4:103443569-103443570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:103442194..103444788-chr4:103454206..103455780,2	MCF-7	breast:
2	chr4:103424918..103427629-chr4:103441760..103444240,2	K562	blood:
3	chr4:103438272..103440503-chr4:103440992..103443713,2	MCF-7	breast:
4	chr4:103421285..103424744-chr4:103439488..103445746,9	MCF-7	breast:
5	chr4:103441543..103444001-chr4:103444588..103447284,2	K562	blood:
6	chr4:103421671..103423440-chr4:103443136..103445338,2	MCF-7	breast:
7	chr4:103442501..103444375-chr4:103444794..103447284,2	K562	blood:
8	chr4:103442159..103444303-chr4:103446884..103449201,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1020759	0.96[CEU][hapmap]
rs1020760	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11722146	0.91[JPT][hapmap]
rs11723120	0.90[JPT][hapmap]
rs118882	0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs12509517	0.91[JPT][hapmap]
rs1585213	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]
rs1585215	1.00[JPT][hapmap]
rs1598856	0.84[CHD][hapmap]
rs1598859	0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs17032705	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]
rs170731	1.00[JPT][hapmap]
rs1801	0.91[JPT][hapmap]
rs2085548	0.85[CHD][hapmap]
rs2168805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs230491	1.00[JPT][hapmap]
rs230492	1.00[JPT][hapmap]
rs230493	1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs230495	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230496	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230498	1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs230500	1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs230504	0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs230505	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs230509	1.00[JPT][hapmap]
rs230514	1.00[JPT][hapmap]
rs230515	1.00[JPT][hapmap]
rs230516	1.00[JPT][hapmap]
rs230519	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs230520	0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs230521	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230525	0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs230526	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs230528	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs230529	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs230531	0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs230532	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs230533	1.00[JPT][hapmap]
rs230534	1.00[JPT][hapmap]
rs230535	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs230539	0.95[JPT][hapmap]
rs230540	0.91[JPT][hapmap]
rs230541	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs230542	0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774936	1.00[JPT][hapmap]
rs3774937	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs3774938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774956	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3774959	0.91[JPT][hapmap];0.83[TSI][hapmap]
rs3774963	0.90[JPT][hapmap]
rs3774964	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4235404	1.00[JPT][hapmap]
rs4648011	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4648055	0.91[JPT][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.91[JPT][hapmap]
rs4698858	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs4699030	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs747559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1599961	COL9A2	trans	multi-tissue	Pritchard
rs1599961	MAPKSP1	cis	cerebellum	SCAN
rs1599961	MANBA	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103423800-103445800	Weak transcription	Lung	lung
2	chr4:103424000-103446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:103425200-103456400	Weak transcription	Osteobl	bone
4	chr4:103425600-103448400	Weak transcription	Fetal Thymus	thymus
5	chr4:103426000-103444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:103426000-103452600	Weak transcription	NH-A	brain
7	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
8	chr4:103426200-103445800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:103426400-103450000	Weak transcription	HMEC	breast
10	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
11	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
13	chr4:103429200-103446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:103431800-103447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
16	chr4:103434000-103446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:103436000-103448600	Weak transcription	HUVEC	blood vessel
18	chr4:103438000-103444200	Weak transcription	Fetal Lung	lung
19	chr4:103438000-103448200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:103438200-103445200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:103438200-103445400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:103438200-103448200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:103438400-103446800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:103438600-103445600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:103438600-103446000	Weak transcription	Fetal Intestine Large	intestine
26	chr4:103439600-103446000	Weak transcription	Primary B cells from cord blood	blood
27	chr4:103439800-103444200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:103439800-103448400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:103440000-103446000	Weak transcription	Esophagus	oesophagus
30	chr4:103440000-103446000	Weak transcription	Stomach Mucosa	stomach
31	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
34	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:103440200-103444200	Weak transcription	HepG2	liver
36	chr4:103440200-103444400	Weak transcription	Right Atrium	heart
37	chr4:103440200-103444600	Weak transcription	Pancreas	Pancrea
38	chr4:103440200-103444600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:103440200-103445600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:103440200-103445600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:103440200-103445800	Weak transcription	Psoas Muscle	Psoas
42	chr4:103440200-103451000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
46	chr4:103440200-103488200	Weak transcription	Gastric	stomach
47	chr4:103440800-103445000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr4:103441000-103445800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:103441000-103448800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:103441200-103448800	Weak transcription	Adipose Nuclei	Adipose

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