Variant report

Variant	rs17376946
Chromosome Location	chr4:85660645-85660646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10516725	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11726731	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs11731505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs11733678	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][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]
rs17009337	1.00[ASN][1000 genomes]
rs17367317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[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];0.85[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17368157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17368458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17368902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[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];0.85[YRI][hapmap]
rs17376293	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376489	0.94[EUR][1000 genomes]
rs17377338	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17377352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17377666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34548715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35767732	0.94[EUR][1000 genomes];1.00[ASN][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];1.00[EUR][1000 genomes];1.00[ASN][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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
2	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
4	chr4:85620800-85663400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85629200-85662400	Weak transcription	Colonic Mucosa	Colon
6	chr4:85633400-85667800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:85640200-85663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:85642800-85668000	Weak transcription	Spleen	Spleen
10	chr4:85642800-85678000	Weak transcription	Gastric	stomach
11	chr4:85646400-85663400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:85648000-85676200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:85651000-85671400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:85651000-85673000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:85651000-85673200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:85651000-85676800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:85651000-85678600	Strong transcription	Placenta	Placenta
18	chr4:85651200-85664400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:85652200-85661600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:85652200-85664000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:85652200-85664800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr4:85652200-85665000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:85652200-85665000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:85652200-85665200	Strong transcription	Adipose Nuclei	Adipose
25	chr4:85652200-85670000	Strong transcription	Liver	Liver
26	chr4:85652200-85678400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:85652200-85678400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:85652200-85679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:85652400-85661000	Strong transcription	Colon Smooth Muscle	Colon
30	chr4:85652400-85661600	Strong transcription	HSMMtube	muscle
31	chr4:85652400-85664800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:85652400-85665000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:85652400-85666600	Strong transcription	HUVEC	blood vessel
34	chr4:85652400-85679200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:85652600-85661800	Strong transcription	NHDF-Ad	bronchial
36	chr4:85652600-85664000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr4:85652600-85664600	Strong transcription	Fetal Lung	lung
38	chr4:85652600-85664800	Strong transcription	NH-A	brain
39	chr4:85652600-85665000	Strong transcription	Brain Anterior Caudate	brain
40	chr4:85652600-85671600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:85652600-85678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:85652600-85678600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:85652800-85661200	Strong transcription	Osteobl	bone
44	chr4:85653200-85667000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:85653600-85664400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:85653800-85660800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:85653800-85661000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:85654800-85663200	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:85655000-85668400	Weak transcription	Fetal Brain Male	brain
50	chr4:85655600-85664800	Strong transcription	HepG2	liver

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