Variant report

Variant	rs6798354
Chromosome Location	chr3:112026480-112026481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10511311	0.84[CEU][hapmap]
rs10804500	0.86[JPT][hapmap]
rs12106673	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs12106967	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13069935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090468	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs13092081	0.98[EUR][1000 genomes]
rs13095299	0.96[EUR][1000 genomes]
rs13098589	0.84[CEU][hapmap]
rs13100916	0.82[EUR][1000 genomes]
rs1317243	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879513	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879514	0.96[ASN][1000 genomes]
rs2272022	0.84[CEU][hapmap]
rs2399412	0.98[EUR][1000 genomes]
rs2399416	0.84[CEU][hapmap]
rs2895395	0.86[JPT][hapmap]
rs4355254	0.86[JPT][hapmap]
rs4682101	0.93[ASN][1000 genomes]
rs4682398	0.96[EUR][1000 genomes]
rs4682399	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs58425909	0.80[ASN][1000 genomes]
rs62278841	0.81[ASN][1000 genomes]
rs62278853	0.80[ASN][1000 genomes]
rs62278855	0.80[ASN][1000 genomes]
rs6438064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780745	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787547	0.97[ASN][1000 genomes]
rs6798486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805117	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805142	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808365	0.99[ASN][1000 genomes]
rs7639471	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7639794	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7647411	0.84[CEU][hapmap]
rs8179893	0.98[EUR][1000 genomes]
rs8179913	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9755930	0.99[ASN][1000 genomes]
rs9814721	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823309	0.99[ASN][1000 genomes]
rs9834347	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9852176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876973	0.93[ASN][1000 genomes]
rs9990215	0.95[CHB][hapmap]
rs9990216	0.91[CHB][hapmap]
rs9990220	0.91[CHB][hapmap]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112023200-112027000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112023200-112027000	Weak transcription	HMEC	breast
3	chr3:112023400-112026600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:112023400-112026800	Weak transcription	Placenta	Placenta
5	chr3:112023400-112027000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:112023400-112027000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:112023400-112027000	Weak transcription	Ovary	ovary
8	chr3:112023400-112027200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:112023600-112027000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:112023600-112027000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:112023600-112027000	Weak transcription	Brain Substantia Nigra	brain
12	chr3:112023600-112027200	Weak transcription	NH-A	brain
13	chr3:112023800-112027000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:112024000-112027000	Weak transcription	Right Atrium	heart
15	chr3:112024000-112028800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:112024200-112027000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:112024200-112027000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:112024200-112027000	Weak transcription	Fetal Thymus	thymus
19	chr3:112024400-112026800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:112024600-112026600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:112024600-112027000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:112024600-112027200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:112024800-112026600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:112024800-112027000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:112025200-112027000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:112025200-112027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:112025200-112027000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:112025200-112027000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:112025200-112027000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:112025200-112034600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:112025400-112027000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:112026200-112027600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:112026400-112026600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:112026400-112027400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:112026400-112027600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:112026400-112027600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:112026400-112027600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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