Variant report

Variant	rs3780453
Chromosome Location	chr9:100964651-100964652
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	chr9:100960639..100963416-chr9:100964074..100967407,4	K562	blood:
2	chr9:100962685..100965590-chr9:101014024..101016888,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10818585	0.81[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]
rs10985377	0.82[AMR][1000 genomes]
rs10985382	0.82[CEU][hapmap]
rs10985441	0.95[GIH][hapmap]
rs2282434	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900463	0.87[GIH][hapmap]
rs3739666	0.86[ASW][hapmap];0.93[GIH][hapmap];0.81[YRI][hapmap]
rs3739667	0.84[GIH][hapmap]
rs3739668	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3780451	0.99[ASN][1000 genomes]
rs3780452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780455	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs3824453	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4237191	0.98[ASN][1000 genomes]
rs4743186	0.93[GIH][hapmap]
rs7029585	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3780453	TBC1D2	cis	parietal	SCAN
rs3780453	HEMGN	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-100965200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:100955800-100965200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:100955800-100970400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:100955800-100970400	Weak transcription	Left Ventricle	heart
5	chr9:100955800-100970400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:100955800-100970600	Weak transcription	Ovary	ovary
7	chr9:100955800-100970600	Weak transcription	Right Ventricle	heart
8	chr9:100955800-100975000	Weak transcription	Primary B cells from cord blood	blood
9	chr9:100955800-100975000	Weak transcription	NHDF-Ad	bronchial
10	chr9:100955800-100975200	Weak transcription	NH-A	brain
11	chr9:100955800-100975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:100956000-100965000	Weak transcription	Adipose Nuclei	Adipose
14	chr9:100956000-100969800	Weak transcription	Primary T cells from cord blood	blood
15	chr9:100956000-100970000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:100956000-100970600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:100956000-100971000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:100956000-100981000	Weak transcription	A549	lung
19	chr9:100956200-100967800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:100956200-100967800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:100956200-100967800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:100956200-100968000	Weak transcription	Stomach Mucosa	stomach
23	chr9:100956200-100970000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:100956200-100973000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:100957000-100967800	Strong transcription	Fetal Intestine Small	intestine
26	chr9:100957800-100968400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:100958000-100967200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:100958200-100967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:100958200-100968400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:100958600-100968200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr9:100959200-100967800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:100959200-100977000	Strong transcription	HMEC	breast
34	chr9:100959600-100984400	Strong transcription	Osteobl	bone
35	chr9:100959800-100965400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:100959800-100966400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr9:100960000-100966200	Strong transcription	Esophagus	oesophagus
39	chr9:100960000-100966400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:100960000-100967200	Strong transcription	Placenta	Placenta
41	chr9:100960000-100967400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:100960000-100967600	Strong transcription	Lung	lung
43	chr9:100960000-100967800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:100960000-100968200	Strong transcription	NHEK	skin
45	chr9:100960200-100965800	Strong transcription	Spleen	Spleen
46	chr9:100960200-100966000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:100960200-100966000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:100960200-100967200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:100960400-100965800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:100960400-100966200	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links