Variant report

Variant	rs3829856
Chromosome Location	chr10:98742750-98742751
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98741127..98743717-chr10:98745929..98748788,2	MCF-7	breast:
2	chr10:98741871..98742756-chr10:98784734..98786018,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11814029	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11815437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11819015	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12571254	0.82[CEU][hapmap]
rs17112206	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17112208	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17112234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17112250	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17112311	0.82[CEU][hapmap]
rs2183447	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28523867	0.88[ASN][1000 genomes]
rs4606419	0.92[ASN][1000 genomes]
rs57437078	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57625543	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57868471	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58550844	0.89[EUR][1000 genomes]
rs72819843	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72819851	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72819853	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72819857	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72819858	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7895214	0.84[CHB][hapmap];0.95[CHD][hapmap]
rs7899594	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7911787	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]

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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3829856	EYA2	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98716600-98743200	Weak transcription	Hela-S3	cervix
2	chr10:98731800-98745600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:98732800-98744200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:98734000-98748400	Weak transcription	Stomach Mucosa	stomach
5	chr10:98734400-98744600	Weak transcription	NHDF-Ad	bronchial
6	chr10:98734600-98746800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:98738000-98743000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:98738400-98744200	Weak transcription	Brain Angular Gyrus	brain
9	chr10:98738800-98744600	Strong transcription	Fetal Intestine Small	intestine
10	chr10:98739200-98744200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:98740200-98743600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:98740200-98743600	Strong transcription	Fetal Intestine Large	intestine
13	chr10:98740400-98742800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr10:98740400-98743000	Strong transcription	Primary B cells from cord blood	blood
15	chr10:98740400-98743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:98740400-98743200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:98740600-98742800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr10:98740600-98742800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr10:98740600-98742800	Strong transcription	Placenta	Placenta
20	chr10:98740600-98742800	Strong transcription	HSMMtube	muscle
21	chr10:98740600-98743000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:98740600-98743000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:98740600-98743000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr10:98740600-98743000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr10:98740600-98743000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:98740600-98743000	Strong transcription	Fetal Lung	lung
27	chr10:98740600-98743000	Strong transcription	Fetal Muscle Leg	muscle
28	chr10:98740600-98743000	Strong transcription	Spleen	Spleen
29	chr10:98740600-98743200	Strong transcription	Liver	Liver
30	chr10:98740600-98743200	Strong transcription	HepG2	liver
31	chr10:98740600-98743400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:98740600-98743600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr10:98740600-98743600	Strong transcription	HSMM	muscle
34	chr10:98740600-98744000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:98740600-98744600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:98740600-98745400	Strong transcription	Fetal Stomach	stomach
37	chr10:98740800-98743200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:98740800-98743400	Strong transcription	NH-A	brain
39	chr10:98741200-98743400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr10:98741200-98743800	Strong transcription	Fetal Brain Female	brain
41	chr10:98741200-98747800	Weak transcription	Psoas Muscle	Psoas
42	chr10:98741200-98758000	Weak transcription	K562	blood
43	chr10:98741600-98743800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:98741600-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr10:98741600-98744000	Weak transcription	Brain Substantia Nigra	brain
46	chr10:98741600-98747600	Weak transcription	Ovary	ovary
47	chr10:98741600-98750600	Weak transcription	NHEK	skin
48	chr10:98741600-98751400	Weak transcription	Small Intestine	intestine
49	chr10:98741800-98745600	Weak transcription	Fetal Brain Male	brain
50	chr10:98741800-98748000	Weak transcription	Colon Smooth Muscle	Colon

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