Variant report

Variant	rs6569048
Chromosome Location	chr6:119431439-119431440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119282106..119284334-chr6:119430594..119433513,2	K562	blood:
2	chr6:119422648..119424264-chr6:119429871..119432417,2	K562	blood:
3	chr6:119412863..119414989-chr6:119430234..119431736,2	K562	blood:
4	chr6:119284022..119285422-chr6:119431250..119432445,6	K562	blood:

Variant related genes	Relation type
ENSG00000111879	Chromatin interaction

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

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

rs_ID	r²[population]
rs1535613	0.95[ASN][1000 genomes]
rs1547829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6569039	1.00[ASN][1000 genomes]
rs6569046	1.00[ASN][1000 genomes]
rs6569047	1.00[ASN][1000 genomes]
rs6569049	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7741875	0.95[ASN][1000 genomes]
rs7746622	0.95[ASN][1000 genomes]
rs7746624	0.95[ASN][1000 genomes]
rs9372522	1.00[ASN][1000 genomes]
rs9374780	0.95[ASN][1000 genomes]
rs9401121	0.95[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	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6569048	MCM9	cis	parietal	SCAN
rs6569048	MCM9	cis	cerebellum	SCAN
rs6569048	FAM184A	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119429600-119431600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:119431000-119431800	Enhancers	Ovary	ovary
3	chr6:119431000-119432000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:119431000-119432000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:119431000-119432200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:119431000-119432400	Enhancers	K562	blood
7	chr6:119431200-119431800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:119431200-119432000	Enhancers	Primary T cells from cord blood	blood
9	chr6:119431200-119432000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr6:119431200-119432000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:119431200-119432000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:119431200-119432000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:119431200-119432000	Enhancers	Fetal Lung	lung
14	chr6:119431200-119432000	Flanking Active TSS	HepG2	liver
15	chr6:119431200-119432200	Enhancers	Brain Anterior Caudate	brain
16	chr6:119431400-119431600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:119431400-119431600	Enhancers	Brain Angular Gyrus	brain
18	chr6:119431400-119431600	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:119431400-119431800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:119431400-119432000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:119431400-119432000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:119431400-119432000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:119431400-119432200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:119431400-119432200	Enhancers	Brain Hippocampus Middle	brain
25	chr6:119431400-119432400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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