Variant report

Variant	rs2299051
Chromosome Location	chr6:15419811-15419812
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	chr6:15418815..15421161-chr6:15421182..15423587,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10484355	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10949294	1.00[JPT][hapmap]
rs10949295	1.00[JPT][hapmap]
rs11756544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11757415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11759478	0.88[JPT][hapmap]
rs12211278	1.00[JPT][hapmap]
rs13192347	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194410	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13195950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13205396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13205612	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13208486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214720	0.89[EUR][1000 genomes]
rs16876278	1.00[JPT][hapmap]
rs16876354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468929	0.88[CEU][hapmap]
rs17575737	0.86[JPT][hapmap]
rs17576233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17576436	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17576710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17637773	1.00[JPT][hapmap]
rs17638192	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17638720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299057	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34002211	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34764533	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35047303	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35139070	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35364784	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629999	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35734069	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35918625	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60416461	0.80[AFR][1000 genomes]
rs61296041	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66478504	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904997	0.95[YRI][hapmap]
rs6914974	0.90[YRI][hapmap]
rs6922136	0.95[YRI][hapmap]
rs6941859	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836327	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7747437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767966	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15401200-15426200	Weak transcription	Pancreas	Pancrea
2	chr6:15403000-15422000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:15404600-15420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:15404600-15421200	Weak transcription	Spleen	Spleen
5	chr6:15404800-15427600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:15404800-15429000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:15405600-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:15405800-15421200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:15409200-15426200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:15410600-15422000	Weak transcription	Gastric	stomach
11	chr6:15412200-15421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:15413000-15420800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:15413600-15421200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:15414200-15421000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:15414200-15421000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:15414200-15421200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:15414200-15422000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:15414200-15422000	Weak transcription	Right Ventricle	heart
19	chr6:15414200-15427200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:15414200-15427400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:15414200-15429200	Weak transcription	HSMM	muscle
22	chr6:15414400-15420000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:15414600-15420800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:15414600-15427800	Weak transcription	Fetal Brain Male	brain
25	chr6:15415000-15421200	Weak transcription	Psoas Muscle	Psoas
26	chr6:15415000-15422200	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:15415400-15420400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr6:15415600-15423400	Weak transcription	Right Atrium	heart
29	chr6:15415800-15421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:15416200-15420400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:15416400-15420000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr6:15416400-15420400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:15417000-15420400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:15417000-15420400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr6:15417000-15420400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:15417000-15420400	ZNF genes & repeats	Dnd41	blood
37	chr6:15417000-15420400	ZNF genes & repeats	K562	blood
38	chr6:15417000-15420600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr6:15417000-15420800	ZNF genes & repeats	GM12878-XiMat	blood
40	chr6:15417000-15452200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr6:15417400-15420800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:15417400-15421200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:15417800-15426800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:15418000-15420800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:15418000-15421000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:15418000-15423200	Weak transcription	Fetal Stomach	stomach
47	chr6:15418200-15420200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:15418400-15420800	Weak transcription	Primary T cells from cord blood	blood
49	chr6:15418400-15420800	Weak transcription	Fetal Heart	heart
50	chr6:15418400-15421000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links