Variant report

Variant	rs12639772
Chromosome Location	chr4:121839403-121839404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10006287	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10026533	0.83[CHB][hapmap]
rs1015219	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10518380	0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11943025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12499872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501914	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12503895	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12507367	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12510578	0.96[ASN][1000 genomes]
rs12511422	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12513227	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12639719	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640648	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644883	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12648660	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397768	0.85[JPT][hapmap]
rs1397771	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1397774	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1450461	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1463785	0.83[CHB][hapmap]
rs1470695	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511302	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1588524	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1597491	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs168226	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17051240	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs17051244	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17051252	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17051254	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17051259	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17051271	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17051275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136999	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2167208	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343182	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs343185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs343189	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3789139	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs3806807	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833182	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4833670	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs4833672	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4833688	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4833689	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57023921	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6813562	0.83[CHB][hapmap]
rs6855578	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs72680432	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72680433	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72680438	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72680440	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72680445	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72680451	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72680462	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680468	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680474	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680476	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680477	0.96[ASN][1000 genomes]
rs72680480	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680484	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680497	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680498	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896060	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs994831	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121798200-121842400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121812800-121839800	Weak transcription	Psoas Muscle	Psoas
3	chr4:121813400-121841600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:121813600-121839800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:121813800-121842400	Weak transcription	NHEK	skin
6	chr4:121814200-121839800	Weak transcription	Pancreas	Pancrea
7	chr4:121814600-121840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
9	chr4:121815200-121839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:121818000-121842400	Weak transcription	NH-A	brain
11	chr4:121821000-121839800	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:121821200-121840000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:121821400-121839800	Weak transcription	Fetal Stomach	stomach
14	chr4:121823800-121842400	Weak transcription	HSMM	muscle
15	chr4:121824800-121840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:121825000-121839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:121825000-121839800	Weak transcription	Osteobl	bone
18	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:121825200-121839800	Weak transcription	Aorta	Aorta
20	chr4:121825600-121842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:121827600-121842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:121828000-121839800	Weak transcription	NHDF-Ad	bronchial
23	chr4:121833600-121839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:121836800-121840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:121837200-121839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:121837200-121839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:121837400-121842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:121838200-121839800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:121838400-121839800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:121838400-121839800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:121838400-121839800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:121838400-121839800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:121838400-121839800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:121838400-121839800	Weak transcription	Left Ventricle	heart
36	chr4:121838400-121839800	Weak transcription	Ovary	ovary
37	chr4:121838400-121840000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr4:121838400-121840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:121838400-121840800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:121838400-121841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:121838400-121841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:121838400-121841200	Weak transcription	NHLF	lung
43	chr4:121838400-121842400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:121838400-121842400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:121838400-121842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:121838400-121842600	Weak transcription	Gastric	stomach
47	chr4:121838600-121842400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:121838800-121842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:121839200-121840600	Enhancers	Fetal Heart	heart
50	chr4:121839200-121841600	Enhancers	Fetal Lung	lung

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