Variant report

Variant	rs9837496
Chromosome Location	chr3:78775567-78775568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10865570	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs11708898	0.91[EUR][1000 genomes]
rs11714414	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11927671	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043662	1.00[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs2118067	1.00[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2164549	1.00[CEU][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes]
rs2255164	0.92[CEU][hapmap]
rs2608023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684377	0.85[EUR][1000 genomes]
rs28429251	0.92[EUR][1000 genomes]
rs28482804	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs510006	0.83[MEX][hapmap]
rs56315536	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769521	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs6785152	1.00[CEU][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes]
rs7619742	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs967454	1.00[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs9834909	0.93[EUR][1000 genomes]
rs984138	1.00[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs9842948	0.87[EUR][1000 genomes]
rs9856624	1.00[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs9864412	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs9874934	1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9875094	1.00[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
3	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78756800-78777800	Weak transcription	Osteobl	bone
5	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:78765800-78778000	Weak transcription	HMEC	breast
10	chr3:78766400-78777400	Weak transcription	Adipose Nuclei	Adipose
11	chr3:78766400-78778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:78766400-78778000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:78766600-78778000	Weak transcription	Ovary	ovary
15	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:78772000-78778000	Weak transcription	NHEK	skin
17	chr3:78772000-78792200	Weak transcription	HepG2	liver
18	chr3:78772800-78776000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:78773000-78775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:78773400-78776200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:78773600-78776000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:78773600-78776200	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:78773800-78776200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:78773800-78776200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:78773800-78777600	Weak transcription	Fetal Brain Male	brain
26	chr3:78774000-78775800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:78774000-78776200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:78774200-78775800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:78774200-78776000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:78774400-78777200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:78774400-78777800	Weak transcription	Fetal Stomach	stomach
32	chr3:78774400-78778000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:78774400-78783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:78774600-78775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:78774600-78775800	Weak transcription	Primary T cells from cord blood	blood
36	chr3:78774600-78777400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:78774800-78776200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:78775000-78775800	Enhancers	Brain Anterior Caudate	brain
39	chr3:78775000-78775800	Weak transcription	Brain Substantia Nigra	brain
40	chr3:78775000-78776200	Enhancers	Brain Hippocampus Middle	brain
41	chr3:78775000-78777800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:78775000-78778000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:78775000-78778000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:78775200-78777400	Weak transcription	Fetal Lung	lung
45	chr3:78775200-78777800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:78775200-78778000	Weak transcription	Fetal Kidney	kidney
47	chr3:78775400-78777400	Weak transcription	A549	lung

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