Variant report

Variant	rs4543747
Chromosome Location	chr1:175977874-175977875
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	chr1:175976933..175978782-chr1:175988459..175991080,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10158829	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10494496	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10737316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10798427	1.00[CHB][hapmap]
rs10798431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10798433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10798435	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10913150	1.00[CHB][hapmap]
rs11803301	0.88[ASN][1000 genomes]
rs11806468	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11809136	1.00[CEU][hapmap]
rs12239888	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1357337	1.00[CHB][hapmap]
rs1522637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16849522	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1831447	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2039231	1.00[CHB][hapmap]
rs2039232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2481627	1.00[CHB][hapmap]
rs2481639	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2481641	1.00[CHB][hapmap]
rs2481647	1.00[CHB][hapmap]
rs2481653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2481657	1.00[CHB][hapmap]
rs2481660	1.00[AMR][1000 genomes]
rs2502822	1.00[CHB][hapmap]
rs2502824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2502825	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2502826	1.00[CHB][hapmap]
rs2502832	1.00[CHB][hapmap]
rs2502834	1.00[CHB][hapmap]
rs2502835	1.00[CHB][hapmap]
rs2502836	1.00[CHB][hapmap]
rs2502841	1.00[CHB][hapmap]
rs2502842	1.00[CHB][hapmap]
rs2861629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3845368	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4304533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4307526	0.81[ASN][1000 genomes]
rs4652140	0.90[ASN][1000 genomes]
rs4652141	0.97[ASN][1000 genomes]
rs4652142	0.97[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap]
rs4652144	0.97[ASN][1000 genomes]
rs4652148	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4652152	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs553852	1.00[CHB][hapmap]
rs559341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs56952885	0.90[ASN][1000 genomes]
rs580978	0.85[CHB][hapmap]
rs58325269	1.00[AMR][1000 genomes]
rs58399286	0.84[ASN][1000 genomes]
rs598177	1.00[AMR][1000 genomes]
rs599326	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs60086820	0.97[ASN][1000 genomes]
rs602933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs61132016	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6425368	1.00[CHB][hapmap]
rs6425370	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6672278	0.90[AMR][1000 genomes]
rs6687043	0.81[ASN][1000 genomes]
rs6688211	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6704509	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs704825	1.00[AMR][1000 genomes]
rs704827	0.85[CHB][hapmap]
rs704830	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs704831	0.90[AMR][1000 genomes]
rs73035644	0.84[ASN][1000 genomes]
rs73035646	0.84[ASN][1000 genomes]
rs73038827	0.97[ASN][1000 genomes]
rs73038833	0.97[ASN][1000 genomes]
rs7517351	1.00[CHB][hapmap]
rs7521561	1.00[CHB][hapmap]
rs7522442	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];0.88[ASN][1000 genomes]
rs7536464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7539247	1.00[CHB][hapmap]
rs7543769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7543882	0.97[ASN][1000 genomes]
rs7545043	1.00[CHB][hapmap]
rs7552181	1.00[CHB][hapmap]
rs7553184	1.00[CHB][hapmap]
rs796933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs796934	1.00[AMR][1000 genomes]
rs9783047	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175946000-175996000	Weak transcription	HMEC	breast
2	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
3	chr1:175954000-175978000	Weak transcription	Left Ventricle	heart
4	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:175957000-175981200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
8	chr1:175958200-175978000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:175958800-175980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:175971400-175981200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:175971600-175981200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:175974000-176003000	Weak transcription	NH-A	brain
14	chr1:175974400-175988200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:175974600-175978000	Weak transcription	Esophagus	oesophagus
16	chr1:175974600-175981800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:175974600-175988800	Weak transcription	Pancreas	Pancrea
18	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:175975200-175978000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:175975400-176003400	Weak transcription	NHLF	lung
21	chr1:175975600-175981200	Weak transcription	Lung	lung
22	chr1:175975600-175981400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:175975600-175988400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:175975800-175978000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:175975800-175980600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:175975800-175988800	Weak transcription	Ovary	ovary
27	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
28	chr1:175976000-175978000	Weak transcription	Fetal Kidney	kidney
29	chr1:175976000-175981600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:175976400-175981000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:175976400-175981000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:175976400-175996000	Weak transcription	HUVEC	blood vessel
33	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:175976600-175978400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:175976800-175978400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:175977000-175978400	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr1:175977000-175978800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:175977200-175978400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:175977200-175978400	ZNF genes & repeats	Fetal Stomach	stomach
42	chr1:175977400-175978000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr1:175977400-175978200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:175977400-175978200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
45	chr1:175977400-175978200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:175977400-175978400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:175977400-175978400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:175977400-175978400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr1:175977400-175978400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:175977400-175978400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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