Variant report

Variant	rs9461153
Chromosome Location	chr6:25393871-25393872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10946770	0.82[EUR][1000 genomes]
rs12201737	0.83[EUR][1000 genomes]
rs716796	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs716798	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs880225	0.82[EUR][1000 genomes]
rs9461152	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9467501	0.83[EUR][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9461153	LRRC16	cis	multi-tissue	Pritchard
rs9461153	LRRC16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25377800-25395600	Weak transcription	Pancreas	Pancrea
3	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
4	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:25388400-25395800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25388400-25396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:25388400-25396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:25389400-25397400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
10	chr6:25390200-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
14	chr6:25390400-25394200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:25390400-25401600	Weak transcription	HMEC	breast
17	chr6:25390800-25397400	Weak transcription	Aorta	Aorta
18	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
19	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:25392000-25398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:25392800-25394400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:25393000-25397200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:25393400-25394400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:25393400-25397200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:25393400-25397400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:25393400-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:25393600-25394000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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