Variant report

Variant	rs10176220
Chromosome Location	chr2:169671161-169671162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11898531	1.00[AMR][1000 genomes]
rs11899247	1.00[AMR][1000 genomes]
rs13383882	0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13384117	1.00[AMR][1000 genomes]
rs13396920	1.00[AMR][1000 genomes]
rs13398166	0.91[AFR][1000 genomes]
rs13402157	1.00[AMR][1000 genomes]
rs28652913	1.00[AMR][1000 genomes]
rs28815499	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73969961	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73969979	1.00[AMR][1000 genomes]
rs9287902	1.00[ASW][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10176220	HMBOX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169659800-169672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:169660000-169676000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:169660000-169688200	Weak transcription	Placenta	Placenta
4	chr2:169661400-169676800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:169662600-169672400	Weak transcription	Gastric	stomach
6	chr2:169662600-169673000	Weak transcription	Left Ventricle	heart
7	chr2:169662600-169675600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:169664400-169672600	Weak transcription	Lung	lung
9	chr2:169667000-169671800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:169667800-169671600	Weak transcription	Adipose Nuclei	Adipose
11	chr2:169667800-169672800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:169668400-169674000	Strong transcription	K562	blood
13	chr2:169668800-169671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:169669200-169672400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:169669400-169671600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:169669400-169671600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:169669400-169673000	Weak transcription	Fetal Intestine Large	intestine
18	chr2:169670000-169671600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:169670000-169672600	Weak transcription	Right Atrium	heart
20	chr2:169670000-169698000	Weak transcription	Stomach Mucosa	stomach
21	chr2:169670200-169690200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:169670400-169671200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:169670400-169671400	Enhancers	Pancreas	Pancrea
24	chr2:169670600-169672200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:169670600-169690800	Weak transcription	Fetal Stomach	stomach
26	chr2:169670800-169671200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:169671000-169672600	Enhancers	Liver	Liver
28	chr2:169671000-169676000	Weak transcription	Duodenum Mucosa	Duodenum

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