Variant report

Variant	rs123509
Chromosome Location	chr3:42733468-42733469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs121993	1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs123506	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339661	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339662	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339682	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339683	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339685	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339686	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs6865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9865715	1.00[CHB][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs123509	HHATL	cis	parietal	SCAN
rs123509	HIGD1A	cis	parietal	SCAN
rs123509	TTC21A	cis	cerebellum	SCAN
rs123509	HHATL	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42725400-42737000	Weak transcription	Right Atrium	heart
2	chr3:42728000-42742800	Weak transcription	Gastric	stomach
3	chr3:42729400-42736800	Weak transcription	Fetal Heart	heart
4	chr3:42729800-42734200	Weak transcription	Right Ventricle	heart
5	chr3:42729800-42737800	Weak transcription	Left Ventricle	heart
6	chr3:42730400-42736600	Weak transcription	HSMMtube	muscle
7	chr3:42731600-42733600	Genic enhancers	Fetal Muscle Leg	muscle
8	chr3:42731600-42734200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr3:42732000-42734200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:42732200-42733800	Enhancers	Brain Hippocampus Middle	brain
11	chr3:42732200-42734800	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:42732400-42733600	Enhancers	Brain Angular Gyrus	brain
13	chr3:42732400-42734200	Enhancers	Brain Anterior Caudate	brain
14	chr3:42732400-42735400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:42732800-42734000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:42732800-42735000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:42733000-42733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:42733400-42734600	Genic enhancers	Brain Substantia Nigra	brain

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Input of quick search could be:

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

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