Variant report

Variant	rs2431238
Chromosome Location	chr5:112124369-112124370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10463643	0.94[GIH][hapmap];0.82[TSI][hapmap]
rs1069061	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs1093677	0.84[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1441375	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs151977	0.86[MEX][hapmap]
rs1661035	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1661036	0.82[EUR][1000 genomes]
rs1734243	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1816769	0.86[CHB][hapmap]
rs187075	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1966477	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2229992	0.81[TSI][hapmap]
rs2431242	0.85[ASN][1000 genomes]
rs2439591	1.00[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2464805	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2545159	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545162	0.84[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2545163	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545164	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2545165	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2545167	0.81[GIH][hapmap]
rs2545169	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2546110	0.82[TSI][hapmap]
rs2546111	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2546116	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2952615	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35130225	0.85[ASN][1000 genomes]
rs351771	0.94[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs382260	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs386830	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs392907	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs395266	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs397768	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs401908	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41115	0.97[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs411356	0.84[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs42427	0.97[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs429427	0.81[GIH][hapmap]
rs430665	0.84[GIH][hapmap]
rs433429	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs434157	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs458967	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs459552	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs464002	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs464708	0.84[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs465899	0.97[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs468179	0.83[EUR][1000 genomes]
rs469727	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs497844	0.91[GIH][hapmap];0.86[MEX][hapmap]
rs501250	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs529076	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544243	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs563556	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs698405	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs712662	0.84[GIH][hapmap]
rs712665	0.84[GIH][hapmap]
rs818427	0.85[CHB][hapmap]
rs866006	0.94[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
5	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:112093400-112128600	Weak transcription	Ovary	ovary
7	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:112097800-112127000	Weak transcription	Esophagus	oesophagus
12	chr5:112098000-112128600	Weak transcription	HepG2	liver
13	chr5:112098200-112128600	Weak transcription	Aorta	Aorta
14	chr5:112098200-112129800	Weak transcription	Spleen	Spleen
15	chr5:112098400-112130000	Weak transcription	Fetal Heart	heart
16	chr5:112098600-112131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:112100000-112152200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:112104400-112125600	Weak transcription	Fetal Intestine Small	intestine
20	chr5:112104600-112128600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:112104600-112155400	Weak transcription	Psoas Muscle	Psoas
22	chr5:112104800-112128000	Weak transcription	Hela-S3	cervix
23	chr5:112104800-112130800	Weak transcription	Stomach Mucosa	stomach
24	chr5:112105000-112128600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:112105000-112128600	Weak transcription	Thymus	Thymus
26	chr5:112105200-112125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:112108200-112129200	Weak transcription	NH-A	brain
28	chr5:112108400-112130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:112110400-112128800	Weak transcription	Brain Angular Gyrus	brain
30	chr5:112111000-112128600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:112112200-112128400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:112112200-112128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:112114000-112128400	Weak transcription	HSMMtube	muscle
34	chr5:112115600-112134600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:112115600-112140000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:112115800-112151200	Weak transcription	NHEK	skin
37	chr5:112116000-112128200	Weak transcription	HMEC	breast
38	chr5:112116000-112128200	Weak transcription	Osteobl	bone
39	chr5:112116200-112126800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:112116800-112129800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:112117000-112130200	Weak transcription	K562	blood
42	chr5:112117800-112128400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:112118000-112126800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:112118000-112127000	Weak transcription	Left Ventricle	heart
45	chr5:112118000-112128400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:112118000-112128600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:112118200-112125000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:112118200-112125400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:112118200-112126600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:112118200-112126800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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