Variant report

Variant	rs2695999
Chromosome Location	chr12:105043923-105043924
allele	C/T
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];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2559638	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2559644	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2694409	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]
rs2694410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694412	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694413	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2694415	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694416	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2695998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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]
rs2696000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2696001	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2696002	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs703658	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs703661	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs727862	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs835482	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs835483	0.81[ASW][hapmap];0.82[MEX][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
rs2695999	UTP20	cis	parietal	SCAN
rs2695999	PMCH	cis	parietal	SCAN

Chromatin state (count:71 , 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	chr12:105024600-105044200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:105033000-105050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:105033400-105050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:105033600-105050200	Weak transcription	Right Atrium	heart
6	chr12:105035000-105045200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:105035400-105050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:105035800-105054000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:105036600-105045200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:105037600-105050200	Weak transcription	Osteobl	bone
11	chr12:105038000-105062000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:105038400-105044000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:105038400-105050400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:105038400-105051600	Weak transcription	Aorta	Aorta
15	chr12:105038400-105053000	Weak transcription	NHEK	skin
16	chr12:105038400-105055400	Weak transcription	Gastric	stomach
17	chr12:105038400-105061200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:105038400-105062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:105038600-105044400	Weak transcription	Left Ventricle	heart
20	chr12:105038600-105045000	Weak transcription	Placenta	Placenta
21	chr12:105038600-105045600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:105038600-105046600	Weak transcription	Pancreas	Pancrea
23	chr12:105038600-105047200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:105038600-105050400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:105038600-105057600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:105038600-105061000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:105038600-105061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:105038600-105062400	Weak transcription	HMEC	breast
29	chr12:105038600-105062800	Weak transcription	Esophagus	oesophagus
30	chr12:105038600-105063200	Weak transcription	Primary T cells from cord blood	blood
31	chr12:105038800-105045600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:105038800-105047200	Weak transcription	K562	blood
33	chr12:105038800-105051000	Weak transcription	GM12878-XiMat	blood
34	chr12:105039200-105062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:105039400-105045200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:105040800-105046800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:105041000-105044200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:105041000-105047800	Weak transcription	Thymus	Thymus
39	chr12:105041200-105048400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr12:105041600-105044000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:105041600-105044800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr12:105041600-105054000	Strong transcription	Dnd41	blood
43	chr12:105041800-105044000	Weak transcription	A549	lung
44	chr12:105041800-105046000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:105041800-105046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:105041800-105046200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:105041800-105048200	Weak transcription	Fetal Thymus	thymus
48	chr12:105042000-105046800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:105042200-105044400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr12:105042600-105044600	Enhancers	Lung	lung

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