Variant report

Variant	rs16833248
Chromosome Location	chr1:151412716-151412717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151412036..151414559-chr1:151416954..151420193,3	MCF-7	breast:
2	1:151411623-151426875..1:151592347-151603110	GM12878	blood:
3	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
4	chr1:151411812..151418574-chr1:151428106..151433466,11	MCF-7	breast:
5	chr1:151410628..151413374-chr1:151426124..151427883,2	MCF-7	breast:
6	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206635	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11204806	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204820	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196346	1.00[CEU][hapmap]
rs1196348	1.00[CEU][hapmap]
rs1196349	1.00[CEU][hapmap]
rs1196351	1.00[CEU][hapmap]
rs1196356	1.00[CEU][hapmap]
rs12566457	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539493	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1571294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16833263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16833274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1781432	1.00[CEU][hapmap]
rs2296840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2997072	1.00[CEU][hapmap]
rs3748549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818561	1.00[CEU][hapmap]
rs4147451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970953	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971045	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56317453	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58057716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59153459	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59848815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587574	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587586	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669679	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67750241	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633634	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72633635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633636	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72633637	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72633638	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72633639	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7548614	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9729256	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv872424	chr1:151325055-151413180	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv872425	chr1:151325055-151413790	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv872429	chr1:151329138-151413180	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv463827	chr1:151333167-151413180	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv547850	chr1:151333167-151413180	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv872430	chr1:151334796-151413180	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv872431	chr1:151338570-151413180	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv872432	chr1:151339196-151413180	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv872433	chr1:151341417-151413180	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv872434	chr1:151347820-151413180	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv872435	chr1:151351060-151413180	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv872436	chr1:151357333-151413180	Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv872437	chr1:151373065-151413180	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
16	nsv872438	chr1:151377407-151413180	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
17	nsv872440	chr1:151396037-151413180	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
18	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151373400-151416400	Weak transcription	Stomach Mucosa	stomach
2	chr1:151393000-151413400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151398600-151417400	Weak transcription	Fetal Heart	heart
5	chr1:151400800-151417400	Weak transcription	Aorta	Aorta
6	chr1:151401000-151416200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
8	chr1:151401400-151413000	Weak transcription	K562	blood
9	chr1:151401400-151413200	Weak transcription	Small Intestine	intestine
10	chr1:151401400-151417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
12	chr1:151402200-151413200	Weak transcription	Fetal Brain Male	brain
13	chr1:151402200-151416200	Weak transcription	Colonic Mucosa	Colon
14	chr1:151403200-151412800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:151403200-151413000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:151403200-151413200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:151403200-151413200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:151403200-151413200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:151403200-151413400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:151403200-151413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:151403200-151413400	Weak transcription	Fetal Kidney	kidney
22	chr1:151403200-151413800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:151403200-151416800	Weak transcription	HSMMtube	muscle
24	chr1:151403400-151413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:151403400-151413200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151403400-151413200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:151403400-151413200	Weak transcription	HUVEC	blood vessel
28	chr1:151403400-151413400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:151403400-151413400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:151403400-151413400	Weak transcription	Pancreas	Pancrea
31	chr1:151403400-151416200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:151403600-151413200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:151403800-151413200	Weak transcription	NH-A	brain
34	chr1:151405800-151428400	Weak transcription	Right Atrium	heart
35	chr1:151406000-151415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:151406200-151414800	Strong transcription	Dnd41	blood
37	chr1:151406400-151415200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:151407800-151413000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:151408200-151413000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:151408200-151413200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:151408200-151413400	Weak transcription	NHLF	lung
42	chr1:151408400-151413200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:151408400-151413200	Weak transcription	NHDF-Ad	bronchial
44	chr1:151408400-151413200	Weak transcription	Osteobl	bone
45	chr1:151408400-151416200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:151408800-151414600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:151408800-151414600	Strong transcription	Fetal Intestine Large	intestine
48	chr1:151408800-151414800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:151408800-151414800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:151409000-151415000	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links