Variant report

Variant	rs6687758
Chromosome Location	chr1:222164948-222164949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222163800..222166412-chr1:222168403..222170793,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10218478	0.82[EUR][1000 genomes]
rs11118926	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12022676	0.91[ASN][1000 genomes]
rs12024555	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025565	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029332	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12032653	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12032715	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033415	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121134	0.92[EUR][1000 genomes]
rs12123928	0.80[EUR][1000 genomes]
rs12124556	0.81[EUR][1000 genomes]
rs12125368	0.91[EUR][1000 genomes]
rs12125383	0.97[EUR][1000 genomes]
rs12129860	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12135286	0.84[EUR][1000 genomes]
rs12137323	0.81[EUR][1000 genomes]
rs12140604	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731064	0.92[EUR][1000 genomes]
rs12739936	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17011141	0.81[EUR][1000 genomes]
rs17011146	0.81[EUR][1000 genomes]
rs17011182	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011200	0.92[EUR][1000 genomes]
rs17442058	0.94[EUR][1000 genomes]
rs17442323	0.92[EUR][1000 genomes]
rs17495159	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2095928	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35212520	0.92[EUR][1000 genomes]
rs35718308	0.85[EUR][1000 genomes]
rs35805428	0.92[EUR][1000 genomes]
rs56170536	0.91[EUR][1000 genomes]
rs66732677	0.91[EUR][1000 genomes]
rs6691195	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695584	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72740077	0.81[EUR][1000 genomes]
rs7520544	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Progressive supranuclear palsy	21685912	GWAS catalog
Colorectal cancer	24836286	GWAS catalog
Colorectal cancer	20972440	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687758	RP11-400N13.2	cis	lung	GTEx
rs6687758	RP11-815M8.1	cis	lung	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222156600-222166000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:222159600-222169400	Enhancers	HMEC	breast
3	chr1:222160400-222165400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:222160400-222165800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:222161000-222165200	Enhancers	NHLF	lung
6	chr1:222161000-222165400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:222161600-222167000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:222162000-222167600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:222162200-222165600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:222162600-222166200	Enhancers	Osteobl	bone
11	chr1:222162800-222165000	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:222162800-222166000	Enhancers	HSMM	muscle
13	chr1:222163000-222165400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:222163000-222165600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:222163200-222165800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:222163200-222165800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:222163400-222165000	Enhancers	NHDF-Ad	bronchial
18	chr1:222163400-222165600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:222163400-222165600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:222163600-222169800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:222163800-222165000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:222163800-222165200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:222163800-222165200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:222163800-222165400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:222163800-222165400	Enhancers	NHEK	skin
26	chr1:222163800-222165600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:222164200-222165600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:222164200-222167200	ZNF genes & repeats	GM12878-XiMat	blood
29	chr1:222164400-222165200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:222164400-222165200	Enhancers	NH-A	brain
31	chr1:222164400-222165400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:222164400-222165600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:222164600-222165600	Enhancers	HSMMtube	muscle
34	chr1:222164800-222165600	Enhancers	Aorta	Aorta

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