Variant report

Variant	rs4589882
Chromosome Location	chr3:24000496-24000497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23958189..23961331-chr3:23997888..24001108,3	MCF-7	breast:
2	chr3:23955851..23960188-chr3:23998337..24001245,6	K562	blood:
3	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:
5	chr3:23995729..23998048-chr3:23998292..24000934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11717862	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631785	0.83[CEU][hapmap]
rs13091509	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13095392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4025822	0.81[EUR][1000 genomes]
rs4131403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241514	0.85[EUR][1000 genomes]
rs4241515	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4241517	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4241520	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4321479	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4619734	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858094	0.92[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858551	0.83[EUR][1000 genomes]
rs4858553	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858565	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858569	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs5023610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs62253379	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419846	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550815	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6550819	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6550823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550824	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550828	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs6550829	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs6764154	0.83[EUR][1000 genomes]
rs6778783	0.85[EUR][1000 genomes]
rs6779476	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793391	0.80[EUR][1000 genomes]
rs6794922	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6807856	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs7371944	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431301	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615255	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs7626431	0.87[CEU][hapmap]
rs7636810	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs7651185	0.83[CEU][hapmap];0.80[GIH][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs9310725	0.83[EUR][1000 genomes]
rs9845287	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs9863320	0.81[EUR][1000 genomes]
rs9879378	0.82[EUR][1000 genomes]
rs9882735	0.97[EUR][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4589882	C3orf48	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
2	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
5	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
7	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
8	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
13	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
14	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:23992000-24001600	Weak transcription	Fetal Stomach	stomach
17	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
18	chr3:23992200-24001200	Weak transcription	Fetal Intestine Large	intestine
19	chr3:23992200-24001400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:23992400-24002400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:23992400-24003400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:23992400-24003400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:23992400-24003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:23993600-24009400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:23993800-24001000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:23995200-24003200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:23995200-24003200	Weak transcription	Dnd41	blood
31	chr3:23995200-24003400	Weak transcription	GM12878-XiMat	blood
32	chr3:23995600-24000800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:23995600-24001000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:23995600-24003200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:23995800-24000800	Weak transcription	Primary B cells from cord blood	blood
36	chr3:23995800-24000800	Weak transcription	Fetal Heart	heart
37	chr3:23995800-24000800	Weak transcription	K562	blood
38	chr3:23995800-24003000	Weak transcription	HepG2	liver
39	chr3:23996000-24001200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:23996000-24012600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:23996200-24001200	Weak transcription	Left Ventricle	heart
42	chr3:23996200-24001800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:23996200-24001800	Strong transcription	Primary T cells from cord blood	blood
44	chr3:23996200-24004800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:23996200-24009400	Weak transcription	Psoas Muscle	Psoas
46	chr3:23996200-24011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:23996200-24021200	Weak transcription	Small Intestine	intestine
48	chr3:23996400-24000600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:23996400-24006200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:23996600-24001200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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