Variant report

Variant	rs3803444
Chromosome Location	chr15:59737506-59737507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-3	chr15:59737408-59737767	NONHSAT044172

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11071447	0.86[CEU][hapmap]
rs11071448	0.84[CEU][hapmap]
rs11071450	0.92[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12439455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4592597	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774331	0.84[CEU][hapmap]
rs4774333	0.84[CEU][hapmap]
rs4774334	0.84[CEU][hapmap]
rs4775168	0.84[CEU][hapmap]
rs4775170	0.84[EUR][1000 genomes]
rs4775171	0.92[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4775173	0.84[CEU][hapmap]
rs6494115	0.84[CEU][hapmap]
rs7175465	0.84[CEU][hapmap]
rs7181716	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs7359171	0.84[CEU][hapmap]
rs8024853	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8024880	0.84[CEU][hapmap]
rs8025175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025871	0.84[CEU][hapmap]
rs8026087	0.84[CEU][hapmap]
rs8028180	0.84[CEU][hapmap]
rs8028913	0.84[CEU][hapmap]
rs8029746	0.84[CEU][hapmap]
rs8030114	0.84[CEU][hapmap]
rs8034709	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
3	nsv904278	chr15:59705005-59784648	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59730800-59754800	Weak transcription	Aorta	Aorta
2	chr15:59731000-59739800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:59731200-59740000	Weak transcription	Stomach Mucosa	stomach
4	chr15:59731400-59752200	Weak transcription	A549	lung
5	chr15:59731600-59753600	Weak transcription	Fetal Brain Female	brain
6	chr15:59731800-59753400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:59732000-59742000	Weak transcription	Fetal Heart	heart
8	chr15:59732200-59744600	Weak transcription	Hela-S3	cervix
9	chr15:59734000-59738600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:59734000-59739400	Weak transcription	Spleen	Spleen
11	chr15:59735400-59753800	Weak transcription	Primary B cells from cord blood	blood
12	chr15:59735800-59737600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:59735800-59738800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:59736400-59738600	Weak transcription	GM12878-XiMat	blood
15	chr15:59736400-59753400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:59736600-59738200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:59736600-59738800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:59736800-59738800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:59736800-59785000	Weak transcription	Fetal Brain Male	brain
20	chr15:59737000-59737600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:59737000-59738600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr15:59737200-59737600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:59737200-59737600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:59737200-59738200	Enhancers	Fetal Lung	lung
25	chr15:59737200-59738800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr15:59737200-59740200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:59737400-59737600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:59737400-59737600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:59737400-59737600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:59737400-59737600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:59737400-59737600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:59737400-59737600	Enhancers	Placenta	Placenta
33	chr15:59737400-59737600	Flanking Active TSS	Ovary	ovary
34	chr15:59737400-59737600	Active TSS	Rectal Smooth Muscle	rectum
35	chr15:59737400-59737600	Flanking Active TSS	Osteobl	bone
36	chr15:59737400-59737800	Active TSS	Fetal Kidney	kidney
37	chr15:59737400-59738000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:59737400-59738800	Enhancers	H9 Cell Line	embryonic stem cell

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