Variant report

Variant	rs742560
Chromosome Location	chr1:210554287-210554288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210550122..210554367-chr1:210555411..210560476,4	K562	blood:
2	chr1:210554011..210556894-chr1:210560022..210561552,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10489388	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12140650	1.00[ASN][1000 genomes]
rs12729428	0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs17016026	0.89[CEU][hapmap];0.89[CHD][hapmap];0.82[EUR][1000 genomes]
rs17759021	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2273009	0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2357583	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765872	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765879	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs60935759	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826890	0.91[EUR][1000 genomes]
rs61828656	0.81[EUR][1000 genomes]
rs6540589	0.89[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes]
rs6656628	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6656669	0.89[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6666446	0.91[EUR][1000 genomes]
rs6669428	0.84[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs6672972	0.97[ASN][1000 genomes]
rs6677509	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs6690120	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7354957	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7355019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527939	0.89[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs7530104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550408	0.82[EUR][1000 genomes]
rs7550554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926582	0.84[EUR][1000 genomes];0.88[ASN][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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs742560	SERTAD4	cis	parietal	SCAN
rs742560	ELK4	cis	cerebellum	SCAN
rs742560	PLXNA2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
2	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
3	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
4	chr1:210543200-210555800	Weak transcription	Right Atrium	heart
5	chr1:210543200-210565200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:210546600-210566200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:210547600-210555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:210548600-210556000	Weak transcription	HepG2	liver
9	chr1:210548600-210566400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:210550200-210557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:210551200-210566600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:210551400-210557600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:210551400-210586000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:210552400-210557800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:210552600-210555000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:210552600-210556000	Weak transcription	HSMMtube	muscle
17	chr1:210552600-210557600	Weak transcription	Osteobl	bone
18	chr1:210552600-210557800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:210552800-210555000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:210552800-210557600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:210552800-210557800	Weak transcription	NHDF-Ad	bronchial
22	chr1:210553000-210557200	Weak transcription	NH-A	brain
23	chr1:210553000-210557400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:210553000-210557600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:210553000-210557600	Weak transcription	NHLF	lung
26	chr1:210553400-210557600	Weak transcription	HSMM	muscle

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