Variant report

Variant	rs11948325
Chromosome Location	chr5:147156861-147156862
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10064237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740989	0.87[JPT][hapmap]
rs12655202	0.87[JPT][hapmap]
rs1549911	0.81[EUR][1000 genomes]
rs2116740	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61162940	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7713108	0.81[EUR][1000 genomes]
rs7719181	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9688059	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs994025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11948325	NLK	trans	parietal	SCAN
rs11948325	CD74	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147146800-147160600	Weak transcription	Primary T cells from cord blood	blood
2	chr5:147147200-147158000	Weak transcription	Brain Germinal Matrix	brain
3	chr5:147147600-147158200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:147148600-147158400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:147148800-147158400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:147151200-147159400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:147151400-147158400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:147151400-147160600	Weak transcription	Fetal Lung	lung
9	chr5:147153000-147158000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:147153000-147158200	Weak transcription	Brain Substantia Nigra	brain
11	chr5:147153000-147159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:147153400-147157600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:147154200-147158400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:147154600-147158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:147154600-147158600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:147154600-147159200	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:147155600-147159600	Weak transcription	Fetal Thymus	thymus
18	chr5:147156000-147161400	Weak transcription	Primary B cells from cord blood	blood
19	chr5:147156200-147159400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:147156200-147161200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:147156400-147159400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:147156400-147159400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:147156600-147157000	Enhancers	HUVEC	blood vessel
24	chr5:147156600-147157200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:147156600-147159800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:147156800-147157000	Enhancers	Brain Angular Gyrus	brain
27	chr5:147156800-147157000	Enhancers	Fetal Brain Male	brain
28	chr5:147156800-147157200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr5:147156800-147158600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:147156800-147159400	Weak transcription	H1 Cell Line	embryonic stem cell

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