Variant report

Variant	rs785143
Chromosome Location	chr6:114645237-114645238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1028299	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12530206	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1359031	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1590320	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1745580	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1745581	0.88[ASN][1000 genomes]
rs1765045	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1765046	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1819198	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997649	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2181437	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2349215	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928891	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785129	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785130	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785131	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs785133	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs785135	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs785139	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs785144	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813063	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374457	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9374460	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9400715	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9400717	0.87[EUR][1000 genomes]
rs975470	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs976271	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs785143	MARCKS	cis	lymphoblastoid	seeQTL
rs785143	MARCKS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114637600-114649600	Weak transcription	Brain Substantia Nigra	brain
2	chr6:114637600-114652200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:114639400-114646000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr6:114640400-114651000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:114641400-114646600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:114642400-114646000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:114642600-114646200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:114643000-114649600	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:114643200-114646400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:114643600-114646400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:114644000-114648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:114644200-114645600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:114644200-114646600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr6:114644400-114645600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:114644400-114651600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:114645200-114645400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:114645200-114646000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:114645200-114649800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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