Variant report

Variant	rs6438066
Chromosome Location	chr3:112027246-112027247
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11714917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716857	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13073116	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17513726	1.00[JPT][hapmap]
rs2280462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2399411	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4234416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4550804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438067	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs6771014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6774405	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6809034	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7619941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs939576	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs939577	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs939578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9814088	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9818526	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3336356	chr3:112027218-112031669	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112024000-112028800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112025200-112034600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:112026200-112027600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:112026400-112027400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112026400-112027600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:112026400-112027600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:112026400-112027600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:112026600-112027400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:112026600-112028400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:112026800-112027400	Enhancers	Placenta	Placenta
11	chr3:112026800-112027600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:112027000-112027400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr3:112027000-112027400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:112027000-112027400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:112027000-112027400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:112027000-112027400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:112027000-112027400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:112027000-112027400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:112027000-112027400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:112027000-112027400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:112027000-112027400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:112027000-112027400	Enhancers	Brain Substantia Nigra	brain
23	chr3:112027000-112027400	Enhancers	Fetal Thymus	thymus
24	chr3:112027000-112027400	Enhancers	Ovary	ovary
25	chr3:112027000-112027400	Enhancers	Right Atrium	heart
26	chr3:112027000-112027400	Enhancers	HMEC	breast
27	chr3:112027000-112027600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:112027000-112027600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112027000-112027600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:112027000-112027600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:112027000-112027600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:112027000-112028000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:112027200-112027400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:112027200-112027400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112027200-112027400	Enhancers	NH-A	brain
36	chr3:112027200-112027600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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