Variant report

Variant	rs17376489
Chromosome Location	chr4:85599858-85599859
allele	G/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:25)

rs_ID	r²[population]
rs10516725	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11726731	0.94[EUR][1000 genomes]
rs11726744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11731505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs11733881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11939816	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1443075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17367317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs17367775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs17368157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17368458	0.94[EUR][1000 genomes]
rs17368902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17375853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs17376048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17376090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs17376293	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs17376461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes]
rs17376946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs17377338	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17377352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17377666	0.94[EUR][1000 genomes]
rs34548715	0.94[EUR][1000 genomes]
rs35767732	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41524654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4569746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85582800-85603000	Weak transcription	Small Intestine	intestine
2	chr4:85586400-85602000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:85586800-85602200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:85587600-85602600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:85587600-85603400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:85587800-85602600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:85587800-85648400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:85588200-85602400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:85588400-85602400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:85588600-85600400	Strong transcription	Adipose Nuclei	Adipose
11	chr4:85588800-85602600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:85589200-85603000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr4:85589400-85602000	Strong transcription	Fetal Intestine Large	intestine
14	chr4:85589400-85609800	Strong transcription	Fetal Brain Female	brain
15	chr4:85589600-85603000	Strong transcription	Liver	Liver
16	chr4:85589600-85604800	Weak transcription	Psoas Muscle	Psoas
17	chr4:85590200-85603000	Strong transcription	Fetal Lung	lung
18	chr4:85592200-85613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:85592400-85602200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:85593200-85602200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:85593200-85603000	Weak transcription	Colonic Mucosa	Colon
22	chr4:85593600-85600800	Strong transcription	Colon Smooth Muscle	Colon
23	chr4:85594200-85602800	Weak transcription	Stomach Mucosa	stomach
24	chr4:85595200-85600200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:85595400-85612600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:85595600-85602800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:85596000-85601600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:85596200-85600200	Strong transcription	Brain Hippocampus Middle	brain
29	chr4:85596200-85634600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:85596400-85600400	Strong transcription	HepG2	liver
31	chr4:85596400-85600800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:85596400-85600800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:85596400-85600800	Strong transcription	NHEK	skin
34	chr4:85596400-85601200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr4:85596400-85602000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:85596400-85602200	Strong transcription	Placenta	Placenta
37	chr4:85596400-85602600	Strong transcription	HSMM	muscle
38	chr4:85596400-85602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:85596400-85602800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr4:85596400-85602800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:85596400-85603000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:85596400-85603000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:85596400-85610200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr4:85596400-85612000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:85596600-85600000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:85596600-85600200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr4:85596600-85600800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:85596600-85601000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:85596600-85601800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:85596600-85602400	Strong transcription	HUVEC	blood vessel

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