Variant report

Variant	rs209846
Chromosome Location	chr16:12415828-12415829
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	chr16:12415388..12417131-chr16:12421455..12424382,2	MCF-7	breast:
2	chr16:12405145..12407568-chr16:12414371..12416056,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11075059	0.81[EUR][1000 genomes]
rs11075061	0.85[EUR][1000 genomes]
rs11075062	0.86[GIH][hapmap]
rs11645864	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11648255	0.88[EUR][1000 genomes]
rs11648926	0.84[EUR][1000 genomes]
rs11861914	0.84[ASN][1000 genomes]
rs12102400	0.82[EUR][1000 genomes]
rs12102608	0.88[EUR][1000 genomes]
rs12148953	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12445263	0.81[EUR][1000 genomes]
rs12445569	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12446650	0.82[EUR][1000 genomes]
rs12448443	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs158467	0.84[AMR][1000 genomes]
rs16959318	0.85[EUR][1000 genomes]
rs176717	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17697005	0.81[EUR][1000 genomes]
rs17764604	0.81[EUR][1000 genomes]
rs209834	0.81[EUR][1000 genomes]
rs209835	0.83[EUR][1000 genomes]
rs209839	0.83[EUR][1000 genomes]
rs209849	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209850	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209851	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209853	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209855	0.90[EUR][1000 genomes]
rs209856	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2856771	0.83[EUR][1000 genomes]
rs289673	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs31679	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35818743	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs476267	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780418	0.81[EUR][1000 genomes]
rs4780422	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780423	0.89[EUR][1000 genomes]
rs4781200	0.81[EUR][1000 genomes]
rs4781201	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4781207	0.90[EUR][1000 genomes]
rs4781208	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4781209	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs4781214	0.89[GIH][hapmap]
rs544598	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62039994	0.90[EUR][1000 genomes]
rs6498278	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6498279	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7184477	0.88[EUR][1000 genomes]
rs7189386	0.81[EUR][1000 genomes]
rs7189945	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7190509	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7192102	0.80[EUR][1000 genomes]
rs7194981	0.83[EUR][1000 genomes]
rs7195981	0.83[EUR][1000 genomes]
rs7199556	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7201621	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs7204209	0.81[EUR][1000 genomes]
rs7204333	0.80[EUR][1000 genomes]
rs8046012	0.82[EUR][1000 genomes]
rs8051758	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8063991	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs868773	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs869289	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9284322	0.88[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs9302469	0.86[EUR][1000 genomes]
rs9939036	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv827555	chr16:12413244-12429978	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
3	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr16:12395600-12417200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr16:12396800-12416400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr16:12404200-12427400	Weak transcription	Primary T cells from cord blood	blood
7	chr16:12405600-12426400	Weak transcription	Lung	lung
8	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
9	chr16:12405800-12417800	Weak transcription	Adipose Nuclei	Adipose
10	chr16:12408800-12417200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr16:12409400-12417400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:12409400-12417600	Weak transcription	Fetal Intestine Small	intestine
13	chr16:12409400-12417800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:12410200-12424400	Weak transcription	Right Atrium	heart
16	chr16:12410200-12464800	Weak transcription	Gastric	stomach
17	chr16:12411600-12416000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:12412200-12416000	Enhancers	HepG2	liver
19	chr16:12412800-12417000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:12413800-12418000	Weak transcription	NHEK	skin
21	chr16:12414200-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:12414400-12416600	Enhancers	Fetal Thymus	thymus
23	chr16:12414400-12417000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:12414400-12417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:12414400-12418000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:12414400-12418200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:12414400-12431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:12414600-12417800	Weak transcription	NHDF-Ad	bronchial
29	chr16:12414600-12418200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr16:12414600-12418200	Weak transcription	Fetal Stomach	stomach
31	chr16:12414800-12416000	Enhancers	Primary B cells from peripheral blood	blood
32	chr16:12414800-12416200	Enhancers	Thymus	Thymus
33	chr16:12414800-12432000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:12415000-12424600	Weak transcription	Esophagus	oesophagus
35	chr16:12415000-12431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:12415200-12416200	ZNF genes & repeats	GM12878-XiMat	blood
37	chr16:12415400-12417800	Weak transcription	Fetal Muscle Leg	muscle
38	chr16:12415400-12435400	Weak transcription	Pancreas	Pancrea
39	chr16:12415600-12417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:12415600-12421400	Weak transcription	Right Ventricle	heart
41	chr16:12415600-12425200	Weak transcription	Primary B cells from cord blood	blood
42	chr16:12415800-12416400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:12415800-12418000	Weak transcription	Left Ventricle	heart
44	chr16:12415800-12421800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links