Variant report

Variant	rs6550823
Chromosome Location	chr3:24013356-24013357
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	chr3:23992186..23994310-chr3:24012801..24015062,2	MCF-7	breast:
2	chr3:24013259..24015464-chr3:24016839..24018635,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11717862	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12631785	0.83[CEU][hapmap]
rs13091509	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13095392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4131403	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241514	0.82[EUR][1000 genomes]
rs4241515	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4241517	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4241520	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4320034	0.89[AFR][1000 genomes]
rs4321479	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4589882	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]
rs4619734	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858094	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4858095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858551	0.80[EUR][1000 genomes]
rs4858553	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4858565	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858569	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]
rs5023610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs62253379	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419846	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550815	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6550819	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550824	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550828	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs6550829	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs6764154	0.80[EUR][1000 genomes]
rs6778783	0.86[EUR][1000 genomes]
rs6779476	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6790557	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793391	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6794922	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6807856	0.80[CEU][hapmap];0.92[TSI][hapmap]
rs7371944	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7431301	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615255	0.87[CEU][hapmap];0.84[GIH][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap]
rs7626431	0.87[CEU][hapmap]
rs7636810	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs7651185	0.83[CEU][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap]
rs9310725	0.85[EUR][1000 genomes]
rs9845287	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9879378	0.84[EUR][1000 genomes]
rs9882735	0.99[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
rs6550823	C3orf48	cis	parietal	SCAN

Chromatin state (count:120 , 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	chr3:24005600-24013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:24005600-24017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:24005600-24032800	Weak transcription	NH-A	brain
30	chr3:24005800-24021400	Strong transcription	Placenta	Placenta
31	chr3:24006200-24019400	Strong transcription	Primary T cells from cord blood	blood
32	chr3:24007800-24013800	Weak transcription	Fetal Thymus	thymus
33	chr3:24007800-24017600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:24007800-24018000	Weak transcription	Thymus	Thymus
35	chr3:24007800-24023200	Weak transcription	Colonic Mucosa	Colon
36	chr3:24008000-24017600	Weak transcription	HSMM	muscle
37	chr3:24008000-24017800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:24008400-24017800	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:24008600-24017600	Weak transcription	Fetal Brain Male	brain
40	chr3:24009000-24015400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr3:24009200-24017800	Weak transcription	Fetal Intestine Small	intestine
42	chr3:24009400-24015000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:24009800-24015000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:24009800-24022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:24010000-24013800	Weak transcription	Fetal Lung	lung
46	chr3:24010000-24017400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:24010000-24017600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:24010200-24013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:24010200-24017400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:24010200-24017600	Weak transcription	Brain Cingulate Gyrus	brain

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