Variant report

Variant	rs321974
Chromosome Location	chr7:78307239-78307240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs170415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs170416	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs170417	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs321971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321972	0.96[ASN][1000 genomes]
rs321978	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs321980	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs321989	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs321990	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs321991	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs38101	0.85[JPT][hapmap]
rs38112	0.85[JPT][hapmap]
rs38118	0.85[JPT][hapmap]
rs413001	0.85[JPT][hapmap]

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	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs321974	HGF	cis	cerebellum	SCAN
rs321974	MDH2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78301800-78321600	Weak transcription	Fetal Brain Female	brain
2	chr7:78304800-78313000	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:78305400-78312400	Weak transcription	Brain Substantia Nigra	brain
4	chr7:78305400-78312800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:78305800-78308200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:78306200-78307400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr7:78306200-78307400	Enhancers	Osteobl	bone
8	chr7:78306400-78307400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:78307000-78307400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr7:78307000-78307400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:78307000-78307400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:78307200-78307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:78307200-78307400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:78307200-78307800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:78307200-78309600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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