Variant report

Variant	rs4562889
Chromosome Location	chr12:50991370-50991371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50990321..50993026-chr12:51018006..51020008,2	K562	blood:
2	chr12:50975463..50977998-chr12:50988989..50993005,3	K562	blood:
3	chr12:50955842..50957766-chr12:50991073..50993827,2	K562	blood:
4	chr12:50896574..50899072-chr12:50989675..50992643,3	K562	blood:
5	chr12:50984762..50986621-chr12:50989741..50991537,2	K562	blood:
6	chr12:50990408..50992631-chr12:51008278..51009960,2	K562	blood:

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10506293	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10506296	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10735826	0.84[ASN][1000 genomes]
rs10783366	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10783367	0.80[ASN][1000 genomes]
rs10783368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876041	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10876044	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10876048	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876054	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876057	0.87[ASN][1000 genomes]
rs10876082	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs11169422	0.81[EUR][1000 genomes]
rs11169551	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11614911	0.82[ASN][1000 genomes]
rs12099511	0.81[EUR][1000 genomes]
rs12099615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12296379	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12307602	0.81[EUR][1000 genomes]
rs12320201	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13328926	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1402693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521515	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1521517	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17119774	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs17124672	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17124888	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17124907	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17531020	1.00[CEU][hapmap]
rs1815010	0.88[AMR][1000 genomes]
rs1996750	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2246840	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2252595	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684890	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs2684891	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2684902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2684906	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28414775	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28479152	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2947617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803181	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3825401	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4129355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4132432	0.90[MEX][hapmap];0.90[AMR][1000 genomes]
rs4143663	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4257057	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4306347	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4450234	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4517607	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768885	0.82[ASN][1000 genomes]
rs4768886	0.82[ASN][1000 genomes]
rs4768887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768894	0.81[ASN][1000 genomes]
rs4768915	0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs56671180	0.81[EUR][1000 genomes]
rs56753963	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56818625	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57283487	0.81[EUR][1000 genomes]
rs57293958	0.81[EUR][1000 genomes]
rs57328764	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57512759	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57578212	0.81[EUR][1000 genomes]
rs57811009	0.81[EUR][1000 genomes]
rs57828015	0.81[EUR][1000 genomes]
rs58301497	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58500867	0.81[EUR][1000 genomes]
rs58888905	0.81[EUR][1000 genomes]
rs58916974	0.81[EUR][1000 genomes]
rs58943330	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59194948	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59284993	0.82[EUR][1000 genomes]
rs59683461	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59696942	0.81[EUR][1000 genomes]
rs59968707	0.81[EUR][1000 genomes]
rs60010359	0.81[EUR][1000 genomes]
rs60198651	0.81[EUR][1000 genomes]
rs60201334	0.81[EUR][1000 genomes]
rs60239257	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60242613	0.81[EUR][1000 genomes]
rs60396677	0.81[EUR][1000 genomes]
rs60420087	0.81[EUR][1000 genomes]
rs60494920	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60743903	0.81[EUR][1000 genomes]
rs60908906	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61578731	0.81[EUR][1000 genomes]
rs6580766	1.00[CEU][hapmap]
rs6580767	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs6580768	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs7131993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132443	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7135222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7302749	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7303202	0.88[AMR][1000 genomes]
rs7304262	0.81[EUR][1000 genomes]
rs7306387	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310507	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7487645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7953880	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7955176	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7955310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7959129	1.00[CEU][hapmap]
rs7969251	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7974480	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7978443	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979184	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979474	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs939631	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs951591	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9634264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9738596	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv1816169	chr12:50973897-51002088	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1817171	chr12:50973897-51002088	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1821299	chr12:50973897-51002088	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1822840	chr12:50973897-51015509	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50968800-50997400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:50969600-50997400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:50974000-51011800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:50975800-50991400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:50976000-50993400	Weak transcription	Fetal Lung	lung
6	chr12:50979200-51013800	Weak transcription	Fetal Stomach	stomach
7	chr12:50979400-50991600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:50979400-50997200	Weak transcription	Pancreas	Pancrea
9	chr12:50979400-50997200	Weak transcription	Spleen	Spleen
10	chr12:50979600-50991400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:50981400-50997400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:50983600-50991600	Weak transcription	HSMMtube	muscle
13	chr12:50983800-50991400	Weak transcription	Adipose Nuclei	Adipose
14	chr12:50984000-50991400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:50987800-50991400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:50988200-50991400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:50988800-50994200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:50989400-50997600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:50989600-50991400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:50989600-50993000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:50989800-50991400	Weak transcription	HepG2	liver
22	chr12:50990000-50991400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:50990000-50992400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:50990000-50992400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:50990200-50992800	Weak transcription	Right Atrium	heart
26	chr12:50990200-50997400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:50990400-50991400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:50990800-50991400	Enhancers	NHEK	skin
29	chr12:50991000-50991400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:50991000-50991400	Enhancers	HUVEC	blood vessel
31	chr12:50991000-50991400	Enhancers	Osteobl	bone
32	chr12:50991000-50991600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:50991000-50991600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:50991000-50991600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:50991000-50991800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:50991000-50991800	Enhancers	Stomach Mucosa	stomach
37	chr12:50991000-50992000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:50991000-50992400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:50991000-50992400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr12:50991000-50992400	Enhancers	K562	blood
41	chr12:50991000-50993000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:50991000-50993000	Enhancers	Left Ventricle	heart
43	chr12:50991200-50991400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50991200-50991400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr12:50991200-50991400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:50991200-50991400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:50991200-50991400	Enhancers	Aorta	Aorta
48	chr12:50991200-50991400	Enhancers	Esophagus	oesophagus
49	chr12:50991200-50991400	Flanking Active TSS	GM12878-XiMat	blood
50	chr12:50991200-50991600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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