Variant report

Variant	rs16962457
Chromosome Location	chr15:49732414-49732415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16962159	1.00[AMR][1000 genomes]
rs16962194	1.00[AMR][1000 genomes]
rs16962260	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs16962301	1.00[AMR][1000 genomes]
rs16962445	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16962483	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2413940	1.00[AMR][1000 genomes]
rs58357997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012342	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012344	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012377	1.00[AMR][1000 genomes]
rs74012379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012381	1.00[AMR][1000 genomes]
rs74012382	1.00[AMR][1000 genomes]
rs74012383	1.00[AMR][1000 genomes]
rs74012386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012389	0.96[AFR][1000 genomes]
rs8035804	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs8035988	1.00[YRI][hapmap]

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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16962457	HBD	trans	lymphoblastoid	seeQTL
rs16962457	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
3	chr15:49725400-49733800	Enhancers	Rectal Smooth Muscle	rectum
4	chr15:49726200-49732800	Enhancers	Fetal Heart	heart
5	chr15:49729000-49733200	Weak transcription	HSMMtube	muscle
6	chr15:49730000-49733800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:49730400-49744600	Weak transcription	NHLF	lung
8	chr15:49730800-49732600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:49731200-49732600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:49731200-49733800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr15:49731600-49733600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:49731600-49733800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:49731600-49734600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:49731600-49734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:49732000-49732600	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:49732000-49736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:49732000-49750200	Weak transcription	HSMM	muscle
18	chr15:49732200-49732600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:49732200-49732800	Enhancers	Osteobl	bone
20	chr15:49732200-49733200	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:49732200-49736200	Weak transcription	Ovary	ovary
22	chr15:49732200-49736200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:49732400-49732800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:49732400-49733400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:49732400-49736800	Weak transcription	Fetal Stomach	stomach
26	chr15:49732400-49738200	Weak transcription	NHDF-Ad	bronchial

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