Variant report

Variant	rs10233497
Chromosome Location	chr7:25348884-25348885
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11760705	0.83[EUR][1000 genomes]
rs11762772	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766628	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770234	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568304	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61361029	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67112407	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721317	0.85[EUR][1000 genomes]
rs916846	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10233497	HOXA2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25339600-25355000	Weak transcription	Fetal Brain Male	brain
2	chr7:25343600-25353800	Weak transcription	Ovary	ovary
3	chr7:25344600-25357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:25344800-25349000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:25345000-25351000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:25346800-25349400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:25346800-25349800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:25347000-25349000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr7:25347000-25351200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:25347400-25352600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:25347600-25349200	Enhancers	Fetal Heart	heart
12	chr7:25347600-25350000	Enhancers	Brain Hippocampus Middle	brain
13	chr7:25347600-25350000	Enhancers	Colon Smooth Muscle	Colon
14	chr7:25347600-25350200	Enhancers	Brain Substantia Nigra	brain
15	chr7:25347600-25350400	Enhancers	Brain Anterior Caudate	brain
16	chr7:25347800-25349000	Enhancers	Brain Germinal Matrix	brain
17	chr7:25347800-25349400	Enhancers	Fetal Muscle Leg	muscle
18	chr7:25347800-25349400	Enhancers	Rectal Smooth Muscle	rectum
19	chr7:25347800-25349600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:25348000-25349200	Enhancers	Duodenum Mucosa	Duodenum
21	chr7:25348000-25349400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:25348200-25349000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:25348200-25349000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:25348200-25349400	Enhancers	Fetal Stomach	stomach
25	chr7:25348200-25351200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr7:25348400-25349200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr7:25348400-25349200	Enhancers	Fetal Intestine Large	intestine
28	chr7:25348400-25349200	Enhancers	Fetal Kidney	kidney
29	chr7:25348400-25349400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr7:25348400-25349400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr7:25348400-25349600	Weak transcription	Pancreas	Pancrea
32	chr7:25348600-25349000	Enhancers	Fetal Lung	lung
33	chr7:25348800-25350000	Weak transcription	Brain Cingulate Gyrus	brain

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