Variant report

Variant	rs4858569
Chromosome Location	chr3:24014314-24014315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23992186..23994310-chr3:24012801..24015062,2	MCF-7	breast:
2	chr3:24013259..24015464-chr3:24016839..24018635,2	MCF-7	breast:
3	chr3:23960526..23962863-chr3:24013920..24016141,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10865791	0.91[JPT][hapmap]
rs11129130	0.91[JPT][hapmap]
rs11717862	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631785	0.83[CEU][hapmap]
rs13091509	0.84[ASN][1000 genomes]
rs13095392	0.83[CHB][hapmap]
rs4078155	0.91[JPT][hapmap]
rs4241515	0.87[ASN][1000 genomes]
rs4241517	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs4241520	0.91[ASN][1000 genomes]
rs4292186	0.91[JPT][hapmap]
rs4293661	0.91[JPT][hapmap]
rs4321479	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4578971	0.91[JPT][hapmap]
rs4589882	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs4858094	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs4858095	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[TSI][hapmap]
rs4858098	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858553	0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4858561	0.91[JPT][hapmap]
rs4858567	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5023610	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6550814	0.84[ASN][1000 genomes]
rs6550815	0.87[ASN][1000 genomes]
rs6550819	0.85[ASN][1000 genomes]
rs6550823	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6779476	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs6794905	0.84[MEX][hapmap]
rs6794922	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.91[ASN][1000 genomes]
rs6807856	0.84[CEU][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs7371944	0.85[MKK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs7431301	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636810	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7646930	0.91[JPT][hapmap]
rs9831760	0.91[JPT][hapmap]
rs9842907	0.82[CEU][hapmap]
rs9845287	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9853532	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9882735	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4858569	C3orf48	cis	parietal	SCAN
rs4858569	TOP2B	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:23996200-24021200	Weak transcription	Small Intestine	intestine
9	chr3:23999800-24019600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:24000000-24020400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:24000800-24019600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:24000800-24021800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:24002600-24017600	Weak transcription	Stomach Mucosa	stomach
14	chr3:24002600-24020200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:24004000-24016400	Weak transcription	Lung	lung
16	chr3:24004000-24017800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:24004000-24017800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:24004000-24017800	Weak transcription	Spleen	Spleen
19	chr3:24004000-24018000	Weak transcription	Esophagus	oesophagus
20	chr3:24004000-24022600	Weak transcription	Aorta	Aorta
21	chr3:24004000-24022600	Weak transcription	Pancreas	Pancrea
22	chr3:24004000-24023400	Weak transcription	Gastric	stomach
23	chr3:24004000-24023800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:24004200-24022600	Weak transcription	Right Ventricle	heart
25	chr3:24005200-24022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:24005400-24017800	Weak transcription	HSMMtube	muscle
27	chr3:24005600-24017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:24005600-24032800	Weak transcription	NH-A	brain
29	chr3:24005800-24021400	Strong transcription	Placenta	Placenta
30	chr3:24006200-24019400	Strong transcription	Primary T cells from cord blood	blood
31	chr3:24007800-24017600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:24007800-24018000	Weak transcription	Thymus	Thymus
33	chr3:24007800-24023200	Weak transcription	Colonic Mucosa	Colon
34	chr3:24008000-24017600	Weak transcription	HSMM	muscle
35	chr3:24008000-24017800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:24008400-24017800	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:24008600-24017600	Weak transcription	Fetal Brain Male	brain
38	chr3:24009000-24015400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:24009200-24017800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:24009400-24015000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr3:24009800-24015000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:24009800-24022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:24010000-24017400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:24010000-24017600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:24010200-24017400	Weak transcription	Brain Substantia Nigra	brain
46	chr3:24010200-24017600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:24010200-24017600	Weak transcription	Fetal Kidney	kidney
48	chr3:24010200-24017600	Weak transcription	GM12878-XiMat	blood
49	chr3:24010200-24017600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:24010200-24017800	Weak transcription	Left Ventricle	heart

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