Variant report

Variant	rs17009618
Chromosome Location	chr4:126336703-126336704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10014217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10084892	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11939811	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504612	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12511204	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512105	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009520	0.85[CHD][hapmap]
rs17009635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009673	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2710562	0.85[CHB][hapmap]
rs2710593	0.86[EUR][1000 genomes]
rs4272024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833325	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58972262	0.83[ASN][1000 genomes]
rs59208392	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840704	0.81[ASN][1000 genomes]
rs73849218	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73849222	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73849223	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs885271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9968420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126311800-126341800	Weak transcription	Fetal Heart	heart
2	chr4:126311800-126343600	Weak transcription	Fetal Stomach	stomach
3	chr4:126312000-126338200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:126312000-126354400	Weak transcription	HSMM	muscle
5	chr4:126312200-126342800	Weak transcription	NHLF	lung
6	chr4:126316600-126354600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:126319000-126338000	Weak transcription	Fetal Brain Female	brain
8	chr4:126319000-126343800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:126320000-126343400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:126320200-126354400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:126320600-126344400	Weak transcription	Lung	lung
12	chr4:126324800-126344400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:126326400-126340800	Weak transcription	Gastric	stomach
14	chr4:126327000-126341800	Weak transcription	Right Ventricle	heart
15	chr4:126327200-126337600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:126329000-126344000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:126329600-126344400	Weak transcription	Fetal Intestine Small	intestine
18	chr4:126329800-126341400	Weak transcription	NHDF-Ad	bronchial
19	chr4:126332600-126337600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:126334600-126390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:126335000-126343600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:126335000-126344000	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:126335200-126342000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:126335200-126353200	Weak transcription	Psoas Muscle	Psoas
25	chr4:126335200-126400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:126335400-126338200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:126335400-126343400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:126335600-126339000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:126335800-126338400	Weak transcription	Brain Germinal Matrix	brain
30	chr4:126335800-126338600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:126335800-126338600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr4:126335800-126340200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:126335800-126340800	Strong transcription	Fetal Lung	lung
34	chr4:126336000-126337000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:126336000-126338600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:126336000-126338600	Strong transcription	Aorta	Aorta
37	chr4:126336000-126338800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr4:126336000-126339000	Strong transcription	Left Ventricle	heart
39	chr4:126336000-126341000	Strong transcription	Ovary	ovary
40	chr4:126336000-126341400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:126336000-126343400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:126336200-126336800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:126336200-126336800	Strong transcription	Fetal Brain Male	brain
44	chr4:126336200-126337400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:126336200-126337800	Strong transcription	Liver	Liver
46	chr4:126336200-126338600	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:126336200-126338600	Strong transcription	HUVEC	blood vessel
48	chr4:126336200-126338800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:126336400-126337000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:126336400-126337800	Strong transcription	Adipose Nuclei	Adipose

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