Variant report

Variant	rs9398518
Chromosome Location	chr6:119933003-119933004
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119932862..119934948-chr6:119935688..119940006,3	K562	blood:
2	chr6:119932562..119937060-chr6:119938471..119941600,5	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12211842	0.94[EUR][1000 genomes]
rs12212125	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12525723	0.93[EUR][1000 genomes]
rs13192985	0.92[EUR][1000 genomes]
rs1572956	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2024731	0.93[EUR][1000 genomes]
rs2064570	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066283	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9372543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9374813	0.93[EUR][1000 genomes]
rs9385081	0.93[EUR][1000 genomes]
rs9401159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401160	0.92[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[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	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027370	chr6:119869409-120056608	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538431	chr6:119869409-120056608	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9398518	COL10A1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119930600-119935200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:119930600-119935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:119930600-119948000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:119930800-119935400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:119930800-119935600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:119931400-119933800	Weak transcription	NHLF	lung
7	chr6:119931800-119933400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:119932200-119934000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:119932200-119934400	Weak transcription	GM12878-XiMat	blood
10	chr6:119932200-119934600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:119932200-119934600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:119932200-119935600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:119932400-119933200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:119932400-119933400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:119932400-119934200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:119932600-119933200	Weak transcription	NHDF-Ad	bronchial
17	chr6:119932800-119933800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:119932800-119933800	Enhancers	Dnd41	blood
19	chr6:119932800-119934000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:119932800-119934200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:119932800-119934600	Enhancers	Ovary	ovary
22	chr6:119932800-119935600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:119933000-119933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:119933000-119933800	Weak transcription	HSMMtube	muscle
25	chr6:119933000-119934000	Weak transcription	NHEK	skin
26	chr6:119933000-119934200	Weak transcription	HMEC	breast

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