Variant report

Variant	rs16908006
Chromosome Location	chr12:12555720-12555721
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12551360..12553535-chr12:12553854..12557038,3	MCF-7	breast:
2	chr12:12550258..12553161-chr12:12554299..12558157,3	MCF-7	breast:
3	chr12:12555144..12557679-chr12:12584651..12587421,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11830917	1.00[CHD][hapmap]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908019	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908222	1.00[CHD][hapmap]
rs17312912	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1861674	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2193270	0.85[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs3741797	1.00[CHD][hapmap]
rs4763288	1.00[JPT][hapmap]
rs4763289	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4763824	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763828	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763831	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4763837	1.00[CHD][hapmap]
rs56261569	0.81[ASN][1000 genomes]
rs58218344	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488523	0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6488524	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6488527	0.85[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7133988	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7134787	1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs7135655	0.83[GIH][hapmap]
rs714480	1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306292	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309982	0.83[GIH][hapmap]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	1.00[ASN][1000 genomes]
rs7973069	1.00[ASN][1000 genomes]
rs7975061	1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs7978842	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7980390	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs888198	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
4	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
12	chr12:12541800-12557200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:12546000-12556400	Weak transcription	K562	blood
15	chr12:12547200-12556000	Weak transcription	Fetal Thymus	thymus
16	chr12:12550000-12556000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:12550000-12556400	Weak transcription	Thymus	Thymus
18	chr12:12550400-12556200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:12551000-12555800	Weak transcription	Primary T cells from cord blood	blood
20	chr12:12551000-12559000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:12551200-12558800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:12551600-12558800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:12551800-12556200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:12552000-12556000	Weak transcription	Fetal Kidney	kidney
25	chr12:12552000-12556000	Weak transcription	HUVEC	blood vessel
26	chr12:12552000-12557800	Weak transcription	Gastric	stomach
27	chr12:12552000-12558800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:12552000-12558800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:12552000-12558800	Weak transcription	Lung	lung
30	chr12:12552000-12559000	Weak transcription	HSMM	muscle
31	chr12:12552000-12559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:12552000-12561400	Weak transcription	HSMMtube	muscle
33	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
34	chr12:12552200-12558600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:12552400-12556200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:12552400-12556200	Weak transcription	Pancreas	Pancrea
37	chr12:12552800-12556800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:12552800-12558600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:12552800-12558800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:12553200-12561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:12553400-12555800	Weak transcription	Fetal Lung	lung
42	chr12:12553400-12556000	Weak transcription	Brain Substantia Nigra	brain
43	chr12:12553400-12556000	Weak transcription	Stomach Mucosa	stomach
44	chr12:12553400-12556200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:12553400-12556200	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:12553400-12556200	Weak transcription	Left Ventricle	heart
47	chr12:12553400-12556200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:12553400-12556600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:12553400-12556800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:12553400-12556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links