Variant report

Variant	rs12645249
Chromosome Location	chr4:148696667-148696668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10027921	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10032488	0.81[EUR][1000 genomes]
rs11099669	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1119887	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs11729081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502667	0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs12640660	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12648074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650280	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116955	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13134018	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13136202	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13136624	0.82[AFR][1000 genomes]
rs13136858	0.83[AFR][1000 genomes]
rs1604785	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17023770	0.82[TSI][hapmap]
rs17023844	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2055551	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118036	0.85[ASW][hapmap];0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2134706	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164527	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6535556	0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs6535558	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6535559	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535560	0.98[AFR][1000 genomes]
rs6535561	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822971	1.00[ASW][hapmap];0.82[CEU][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6829479	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6836509	0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs6837391	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6839987	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs6840039	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6845560	1.00[ASW][hapmap];0.82[CEU][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7673234	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7673606	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332471	0.92[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964170	1.00[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880242	chr4:148659137-148727355	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148689400-148698000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:148689600-148700200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:148689800-148699400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:148689800-148700400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:148691200-148696800	Enhancers	Psoas Muscle	Psoas
6	chr4:148691400-148697800	Enhancers	Fetal Intestine Small	intestine
7	chr4:148692200-148696800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:148692400-148697600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:148693200-148697000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:148693200-148700600	Enhancers	Colon Smooth Muscle	Colon
11	chr4:148693400-148697000	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr4:148693400-148697800	Weak transcription	Pancreas	Pancrea
13	chr4:148693600-148697200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr4:148693600-148697400	Weak transcription	Esophagus	oesophagus
15	chr4:148693800-148697400	Enhancers	Stomach Smooth Muscle	stomach
16	chr4:148693800-148697600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:148693800-148697800	Weak transcription	Gastric	stomach
18	chr4:148693800-148699800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:148694600-148699400	Enhancers	Fetal Muscle Leg	muscle
20	chr4:148694800-148697000	Genic enhancers	HSMM	muscle
21	chr4:148694800-148698000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:148694800-148708400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:148695000-148696800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:148695000-148696800	Enhancers	Ovary	ovary
25	chr4:148695000-148696800	Enhancers	HUVEC	blood vessel
26	chr4:148695000-148699600	Enhancers	Left Ventricle	heart
27	chr4:148695200-148697800	Weak transcription	Stomach Mucosa	stomach
28	chr4:148695200-148698600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:148695200-148698600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:148695200-148698600	Weak transcription	Osteobl	bone
31	chr4:148695200-148701400	Weak transcription	Small Intestine	intestine
32	chr4:148695400-148707400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:148695600-148697200	Enhancers	HSMMtube	muscle
34	chr4:148695600-148697800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:148695600-148697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:148695600-148697800	Weak transcription	Aorta	Aorta
37	chr4:148695600-148697800	Weak transcription	NHEK	skin
38	chr4:148695600-148698000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:148695600-148698000	Weak transcription	NHDF-Ad	bronchial
40	chr4:148695600-148699200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:148695600-148699400	Weak transcription	Adipose Nuclei	Adipose
42	chr4:148695600-148700000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:148695600-148706400	Weak transcription	Fetal Stomach	stomach
44	chr4:148695800-148697800	Enhancers	Duodenum Mucosa	Duodenum
45	chr4:148695800-148697800	Weak transcription	NHLF	lung
46	chr4:148696000-148697800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:148696000-148698000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:148696000-148698000	Weak transcription	HMEC	breast
49	chr4:148696000-148698600	Weak transcription	NH-A	brain
50	chr4:148696000-148698800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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