Variant report

Variant	rs2694409
Chromosome Location	chr12:105045333-105045334
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	chr12:105043561..105045701-chr12:105049277..105051799,2	MCF-7	breast:
2	chr12:105040332..105041900-chr12:105043587..105045968,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1863879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2559638	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2559644	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694410	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694411	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694412	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694413	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2694415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694416	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2695998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2695999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2696000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2696001	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2696002	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs703658	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs703661	1.00[ASW][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs727862	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs835482	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs835483	0.81[ASW][hapmap];0.86[TSI][hapmap]
rs861346	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2694409	UTP20	cis	parietal	SCAN
rs2694409	PMCH	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105022400-105048200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:105033000-105050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:105033400-105050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:105033600-105050200	Weak transcription	Right Atrium	heart
5	chr12:105035400-105050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:105035800-105054000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:105037600-105050200	Weak transcription	Osteobl	bone
8	chr12:105038000-105062000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:105038400-105050400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:105038400-105051600	Weak transcription	Aorta	Aorta
11	chr12:105038400-105053000	Weak transcription	NHEK	skin
12	chr12:105038400-105055400	Weak transcription	Gastric	stomach
13	chr12:105038400-105061200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:105038400-105062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:105038600-105045600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:105038600-105046600	Weak transcription	Pancreas	Pancrea
17	chr12:105038600-105047200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:105038600-105050400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:105038600-105057600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:105038600-105061000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:105038600-105061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:105038600-105062400	Weak transcription	HMEC	breast
23	chr12:105038600-105062800	Weak transcription	Esophagus	oesophagus
24	chr12:105038600-105063200	Weak transcription	Primary T cells from cord blood	blood
25	chr12:105038800-105045600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:105038800-105047200	Weak transcription	K562	blood
27	chr12:105038800-105051000	Weak transcription	GM12878-XiMat	blood
28	chr12:105039200-105062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:105040800-105046800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:105041000-105047800	Weak transcription	Thymus	Thymus
31	chr12:105041200-105048400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:105041600-105054000	Strong transcription	Dnd41	blood
33	chr12:105041800-105046000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:105041800-105046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:105041800-105046200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:105041800-105048200	Weak transcription	Fetal Thymus	thymus
37	chr12:105042000-105046800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:105042600-105045600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:105042600-105046000	Enhancers	Adipose Nuclei	Adipose
40	chr12:105042800-105046200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:105042800-105046800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:105042800-105047400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:105043000-105054000	Weak transcription	Brain Angular Gyrus	brain
44	chr12:105043200-105046800	Enhancers	Brain Anterior Caudate	brain
45	chr12:105043400-105045800	Weak transcription	Primary B cells from cord blood	blood
46	chr12:105043400-105046000	Enhancers	Fetal Brain Female	brain
47	chr12:105043600-105045600	Enhancers	Brain Germinal Matrix	brain
48	chr12:105043600-105046200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:105043600-105046400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr12:105043600-105046600	Enhancers	Fetal Brain Male	brain

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