Variant report

Variant	rs1144346
Chromosome Location	chr1:76552475-76552476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11162079	0.88[ASN][1000 genomes]
rs1144343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146663	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251576	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1251806	0.87[ASN][1000 genomes]
rs12568806	0.92[ASN][1000 genomes]
rs1417407	0.92[ASN][1000 genomes]
rs1763465	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291075	0.95[ASN][1000 genomes]
rs699829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs699830	0.95[ASN][1000 genomes]

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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1144346	ACADM	cis	parietal	SCAN
rs1144346	ACADM	cis	cerebellum	SCAN
rs1144346	MSH4	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542200-76553200	Weak transcription	Fetal Intestine Large	intestine
2	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
4	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
5	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:76549000-76556200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:76549000-76556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:76549200-76552800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:76549200-76556600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:76549200-76556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:76550000-76556600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:76550200-76556800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:76551200-76552600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:76551200-76553000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:76551200-76556200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:76551400-76554000	Enhancers	Fetal Lung	lung
17	chr1:76551400-76556000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:76551400-76556000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:76551600-76552600	Enhancers	HUVEC	blood vessel
20	chr1:76551600-76554400	Enhancers	Stomach Mucosa	stomach
21	chr1:76552000-76553800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:76552200-76552600	Enhancers	Brain Substantia Nigra	brain
23	chr1:76552200-76552600	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:76552200-76553000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:76552200-76553200	Enhancers	Fetal Kidney	kidney
26	chr1:76552200-76553400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:76552200-76553400	Enhancers	Fetal Stomach	stomach
28	chr1:76552200-76554200	Enhancers	Fetal Intestine Small	intestine
29	chr1:76552400-76552800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:76552400-76553200	Enhancers	Colon Smooth Muscle	Colon
31	chr1:76552400-76553200	Enhancers	Rectal Smooth Muscle	rectum

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