Variant report

Variant	rs7784067
Chromosome Location	chr7:31084099-31084100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11973216	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13246826	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023120	chr7:30655070-31185096	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2761316	chr7:30655082-31166676	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv527038	chr7:30657467-31161945	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv916877	chr7:30661135-31154731	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1017168	chr7:30663213-31166676	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1017808	chr7:30671936-31150473	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv464418	chr7:31072386-31116168	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv606522	chr7:31072386-31116168	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv606523	chr7:31074214-31122542	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7784067	HOXA1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:31063400-31086800	Weak transcription	Spleen	Spleen
2	chr7:31081800-31085000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:31082000-31085000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:31082000-31085000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr7:31082200-31084400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:31082200-31084400	Enhancers	Brain Germinal Matrix	brain
7	chr7:31082200-31085200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:31082400-31085000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:31082400-31085200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:31082800-31085000	Enhancers	Fetal Muscle Leg	muscle
11	chr7:31082800-31086600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:31083000-31084400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:31083000-31084800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:31083000-31091200	Weak transcription	Fetal Brain Male	brain
15	chr7:31083200-31089200	Weak transcription	Fetal Brain Female	brain
16	chr7:31083400-31085000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:31083400-31086600	Weak transcription	Brain Anterior Caudate	brain
18	chr7:31083600-31088000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:31084000-31084600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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