Variant report

Variant	rs679840
Chromosome Location	chr1:212686682-212686683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212683483..212692182-chr1:212779770..212786326,12	K562	blood:
2	chr1:212686498..212689410-chr1:212730977..212733279,2	MCF-7	breast:
3	chr1:212675568..212680156-chr1:212685148..212688870,4	K562	blood:
4	chr1:212685711..212688153-chr1:212791617..212793606,2	K562	blood:
5	chr1:212663187..212667039-chr1:212686323..212689300,3	K562	blood:
6	chr1:212683483..212690052-chr1:212778903..212785088,8	K562	blood:
7	chr1:212685969..212688191-chr1:212785458..212787889,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260805	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12131037	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12135668	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12141407	0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs12729438	0.91[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12753186	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12754528	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13374785	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2005230	0.82[ASN][1000 genomes]
rs2292479	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2292481	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2292482	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001262	0.98[EUR][1000 genomes]
rs34543166	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36056520	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3951316	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs525176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557252	0.98[EUR][1000 genomes]
rs591176	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626178	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs638527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669813	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704297	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs748517	0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7513550	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517259	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7519767	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7529867	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553229	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806539	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9430096	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
7	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs679840	TMEM206	cis	cerebellum	SCAN
rs679840	TMEM206	cis	parietal	SCAN
rs679840	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs679840	RPS6KC1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212681000-212686800	Weak transcription	Right Atrium	heart
2	chr1:212681000-212688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:212682600-212687400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:212685200-212689000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:212685400-212688000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:212685600-212687600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr1:212685800-212687600	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr1:212686200-212687400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr1:212686200-212687600	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr1:212686200-212687800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:212686200-212687800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
12	chr1:212686200-212687800	Bivalent Enhancer	HSMM	muscle
13	chr1:212686200-212687800	Enhancers	HSMMtube	muscle
14	chr1:212686200-212688200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:212686200-212688400	Enhancers	NH-A	brain
16	chr1:212686400-212686800	Enhancers	Aorta	Aorta
17	chr1:212686400-212687400	Flanking Active TSS	Hela-S3	cervix
18	chr1:212686400-212687400	Bivalent Enhancer	HMEC	breast
19	chr1:212686400-212687600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:212686400-212687600	Enhancers	Right Ventricle	heart
21	chr1:212686400-212687600	Enhancers	Spleen	Spleen
22	chr1:212686400-212687800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:212686400-212687800	Bivalent Enhancer	NHLF	lung
24	chr1:212686400-212688000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:212686400-212688000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:212686400-212688000	Bivalent Enhancer	Placenta	Placenta
27	chr1:212686400-212688000	Enhancers	Left Ventricle	heart
28	chr1:212686400-212688400	Enhancers	Pancreas	Pancrea
29	chr1:212686600-212686800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:212686600-212687400	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:212686600-212687400	Flanking Active TSS	A549	lung
32	chr1:212686600-212687600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:212686600-212688000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin

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