Variant report

Variant	rs502399
Chromosome Location	chr3:43105018-43105019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11707627	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11707725	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715255	0.83[EUR][1000 genomes]
rs11719573	0.83[CEU][hapmap];0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs17075162	0.83[EUR][1000 genomes]
rs1851577	0.83[EUR][1000 genomes]
rs28376397	0.81[EUR][1000 genomes]
rs545023	1.00[JPT][hapmap]
rs57549659	0.82[EUR][1000 genomes]
rs615538	0.86[EUR][1000 genomes]
rs62247988	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62247992	0.87[EUR][1000 genomes]
rs627582	0.84[EUR][1000 genomes]
rs737351	0.83[CEU][hapmap];0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs7619872	0.83[EUR][1000 genomes]
rs834175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs502399	FYCO1	cis	parietal	SCAN
rs502399	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:43102800-43118800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:43103400-43105400	Strong transcription	Liver	Liver
13	chr3:43104200-43105400	Enhancers	Dnd41	blood
14	chr3:43104200-43106000	Strong transcription	Ovary	ovary
15	chr3:43104200-43106400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:43104400-43105600	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr3:43104400-43106400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr3:43104400-43106600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:43104600-43106200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:43104600-43106200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:43104800-43105400	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr3:43104800-43120800	Weak transcription	Gastric	stomach
23	chr3:43105000-43105400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:43105000-43105600	Strong transcription	Placenta	Placenta
25	chr3:43105000-43105600	Weak transcription	Fetal Stomach	stomach
26	chr3:43105000-43118800	Weak transcription	Thymus	Thymus
27	chr3:43105000-43119600	Weak transcription	Stomach Smooth Muscle	stomach

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