Variant report

Variant	rs12499541
Chromosome Location	chr4:48181172-48181173
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10805164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10805165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11730441	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs11945978	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs12502268	0.96[ASN][1000 genomes]
rs12512766	0.81[ASN][1000 genomes]
rs12512837	0.96[ASN][1000 genomes]
rs13104849	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1466990	0.89[ASN][1000 genomes]
rs1466991	0.96[ASN][1000 genomes]
rs1466992	0.96[ASN][1000 genomes]
rs1466993	0.96[ASN][1000 genomes]
rs1466994	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs1466995	0.93[ASN][1000 genomes]
rs1466996	0.96[ASN][1000 genomes]
rs1507919	1.00[JPT][hapmap]
rs1961974	0.96[ASN][1000 genomes]
rs1961975	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs2089509	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs2089510	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2089511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2243840	1.00[JPT][hapmap]
rs2271173	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs2271174	0.91[ASN][1000 genomes]
rs2661529	1.00[JPT][hapmap]
rs2661543	0.81[ASN][1000 genomes]
rs2661544	0.81[ASN][1000 genomes]
rs2661547	1.00[JPT][hapmap]
rs2661548	1.00[JPT][hapmap]
rs2704399	1.00[JPT][hapmap]
rs2704426	1.00[JPT][hapmap]
rs2704433	0.81[ASN][1000 genomes]
rs2704436	0.85[JPT][hapmap]
rs3792620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3792621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3792622	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs3805179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3805184	1.00[JPT][hapmap]
rs3913948	0.91[ASN][1000 genomes]
rs4323077	0.96[ASN][1000 genomes]
rs4392481	0.96[ASN][1000 genomes]
rs4392482	0.96[ASN][1000 genomes]
rs4504220	0.89[ASN][1000 genomes]
rs4695339	0.96[ASN][1000 genomes]
rs4695340	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs4695341	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4695342	0.96[ASN][1000 genomes]
rs4695343	0.96[ASN][1000 genomes]
rs4695344	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs4695346	0.96[ASN][1000 genomes]
rs4695347	0.96[ASN][1000 genomes]
rs4695348	0.96[ASN][1000 genomes]
rs4695349	0.96[ASN][1000 genomes]
rs4695350	0.96[ASN][1000 genomes]
rs61326763	0.91[ASN][1000 genomes]
rs62309327	0.96[ASN][1000 genomes]
rs6447616	1.00[JPT][hapmap]
rs6814443	1.00[JPT][hapmap]
rs6845941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6851861	0.96[ASN][1000 genomes]
rs7654108	0.96[ASN][1000 genomes]
rs7668350	0.96[ASN][1000 genomes]
rs7669393	0.96[ASN][1000 genomes]
rs7670351	0.96[ASN][1000 genomes]
rs7671720	0.93[ASN][1000 genomes]
rs7689953	1.00[JPT][hapmap]
rs7695902	0.96[ASN][1000 genomes]
rs7696119	0.96[ASN][1000 genomes]
rs7696271	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1006853	chr4:48164958-48196335	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1011820	chr4:48170669-48186729	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1011366	chr4:48173947-48186644	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1005668	chr4:48173947-48186729	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
3	chr4:48169000-48190000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48170600-48181200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:48171200-48181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:48173800-48188400	Weak transcription	Lung	lung
7	chr4:48175800-48191600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:48176000-48185200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:48176000-48185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:48176000-48185400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:48176200-48185200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:48177600-48182200	Weak transcription	HSMM	muscle
13	chr4:48177800-48181600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr4:48178000-48192400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:48178200-48182200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:48178200-48185200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:48178800-48185400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:48179600-48182200	ZNF genes & repeats	GM12878-XiMat	blood
19	chr4:48180000-48181200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr4:48180200-48183200	Enhancers	Fetal Thymus	thymus
21	chr4:48180400-48181200	Enhancers	Thymus	Thymus
22	chr4:48180600-48181200	Enhancers	H9 Cell Line	embryonic stem cell
23	chr4:48180600-48181200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr4:48180800-48181200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:48180800-48181400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:48180800-48182400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:48180800-48182400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:48180800-48187800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:48181000-48181200	Enhancers	Pancreas	Pancrea
30	chr4:48181000-48182000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:48181000-48185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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