Variant report

Variant	rs10985441
Chromosome Location	chr9:100970881-100970882
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	chr9:100968715..100971359-chr9:101017850..101020097,2	MCF-7	breast:
2	chr9:100743176..100746592-chr9:100969573..100972720,3	K562	blood:

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10818669	0.83[AMR][1000 genomes]
rs10985366	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1469800	0.81[AMR][1000 genomes]
rs1469802	0.82[AMR][1000 genomes]
rs2023361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181581	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2417893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900463	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739664	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739665	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs3739666	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780449	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780452	0.95[GIH][hapmap]
rs3780453	0.95[GIH][hapmap]
rs4743186	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478596	0.82[ASN][1000 genomes]
rs6478597	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7021760	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029585	0.93[GIH][hapmap]
rs733040	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7850360	0.83[AMR][1000 genomes]
rs7855855	0.95[CHB][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs942166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10985441	TBC1D2	cis	cerebellum	SCAN
rs10985441	TBC1D2	cis	multi-tissue	Pritchard
rs10985441	CORO2A	cis	Whole Blood	GTEx
rs10985441	TBC1D2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-100975000	Weak transcription	Primary B cells from cord blood	blood
2	chr9:100955800-100975000	Weak transcription	NHDF-Ad	bronchial
3	chr9:100955800-100975200	Weak transcription	NH-A	brain
4	chr9:100955800-100975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:100956000-100971000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:100956000-100981000	Weak transcription	A549	lung
8	chr9:100956200-100973000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:100959200-100977000	Strong transcription	HMEC	breast
11	chr9:100959600-100984400	Strong transcription	Osteobl	bone
12	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
14	chr9:100962000-100972600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:100962600-100975200	Weak transcription	Brain Anterior Caudate	brain
16	chr9:100962800-100971000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:100964400-100971000	Weak transcription	Pancreas	Pancrea
18	chr9:100965600-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:100965800-100971000	Weak transcription	Adipose Nuclei	Adipose
20	chr9:100965800-100971000	Weak transcription	Colonic Mucosa	Colon
21	chr9:100968000-100987000	Weak transcription	Small Intestine	intestine
22	chr9:100968200-100971000	Genic enhancers	NHEK	skin
23	chr9:100968200-100976400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr9:100968400-100971000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:100968400-100971400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:100968400-100972000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:100968400-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:100968600-100971000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:100968600-100971200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr9:100968600-100971200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:100968600-100971200	Weak transcription	Liver	Liver
34	chr9:100968600-100985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:100968800-100973000	Weak transcription	Stomach Mucosa	stomach
37	chr9:100968800-100973600	Weak transcription	HepG2	liver
38	chr9:100968800-100975200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:100968800-100984600	Weak transcription	K562	blood
40	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr9:100969000-100979000	Weak transcription	Fetal Brain Female	brain
43	chr9:100969000-100984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:100969200-100976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:100969200-100985600	Strong transcription	Fetal Intestine Small	intestine
46	chr9:100969400-100980600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:100969400-100981000	Strong transcription	Placenta	Placenta
48	chr9:100969400-100981000	Weak transcription	Fetal Thymus	thymus
49	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
50	chr9:100969600-100971000	Strong transcription	Fetal Intestine Large	intestine

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