Variant report

Variant	rs11762772
Chromosome Location	chr7:25344021-25344022
allele	A/G
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]
rs10233497	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760705	0.83[EUR][1000 genomes]
rs11766628	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770234	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568304	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61361029	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67112407	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721317	0.85[EUR][1000 genomes]
rs916846	0.91[AFR][1000 genomes];1.00[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
rs11762772	HOXA2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25339600-25355000	Weak transcription	Fetal Brain Male	brain
2	chr7:25342400-25344200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr7:25342400-25344600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:25342400-25344600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr7:25342600-25344600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:25342600-25344600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:25342600-25344600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:25342600-25344800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:25342600-25344800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:25342600-25345000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr7:25342800-25344400	Enhancers	Brain Germinal Matrix	brain
12	chr7:25342800-25344800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:25343000-25344800	Enhancers	Fetal Muscle Leg	muscle
14	chr7:25343000-25345000	Enhancers	Fetal Stomach	stomach
15	chr7:25343200-25344400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:25343200-25344400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:25343200-25344800	Enhancers	Fetal Intestine Small	intestine
18	chr7:25343200-25344800	Enhancers	Fetal Lung	lung
19	chr7:25343200-25347000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:25343200-25347600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:25343200-25348000	Weak transcription	Pancreas	Pancrea
22	chr7:25343400-25344400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:25343400-25344400	Weak transcription	Right Atrium	heart
24	chr7:25343400-25344600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr7:25343400-25344600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:25343600-25344200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:25343600-25344400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr7:25343600-25344400	Weak transcription	Spleen	Spleen
29	chr7:25343600-25344600	Weak transcription	Lung	lung
30	chr7:25343600-25346800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:25343600-25348400	Weak transcription	Fetal Kidney	kidney
32	chr7:25343600-25353800	Weak transcription	Ovary	ovary
33	chr7:25343800-25344800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr7:25343800-25346000	Enhancers	Fetal Heart	heart
35	chr7:25343800-25347600	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:25343800-25347800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:25343800-25347800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr7:25343800-25348400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:25344000-25344400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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