Variant report

Variant	rs4657613
Chromosome Location	chr1:166870878-166870879
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	chr1:166869400..166871863-chr1:166876287..166879217,2	K562	blood:

Variant related genes	Relation type
ENSG00000237096	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10800270	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10800276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918599	0.89[EUR][1000 genomes]
rs10918600	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10918603	0.83[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11579987	0.88[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs11583927	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11584352	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562794	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1476347	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs1543313	0.94[ASN][1000 genomes]
rs2072740	0.93[ASN][1000 genomes]
rs2072742	0.81[EUR][1000 genomes]
rs2075946	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs2142615	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2223221	0.99[ASN][1000 genomes]
rs2235184	0.94[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2280995	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294195	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2312675	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs34381372	0.97[ASN][1000 genomes]
rs3820387	0.88[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs4656516	0.97[ASN][1000 genomes]
rs4657609	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657612	0.99[ASN][1000 genomes]
rs61815130	0.88[EUR][1000 genomes]
rs61815132	0.88[EUR][1000 genomes]
rs6427047	0.94[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs742048	0.88[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7513457	0.99[ASN][1000 genomes]
rs7545806	0.83[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs9633326	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4657613	B4GALT3	cis	parietal	SCAN
rs4657613	RGS4	cis	parietal	SCAN
rs4657613	DUSP12	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166867200-166876800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:166867800-166873600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:166869400-166871800	Enhancers	Fetal Muscle Leg	muscle
4	chr1:166869600-166871000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:166870200-166871000	Enhancers	HSMMtube	muscle
6	chr1:166870200-166871200	Enhancers	Rectal Smooth Muscle	rectum
7	chr1:166870200-166871400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:166870200-166872800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:166870200-166875400	Enhancers	Placenta	Placenta
10	chr1:166870400-166871000	Active TSS	Small Intestine	intestine
11	chr1:166870400-166871000	Weak transcription	K562	blood
12	chr1:166870400-166871200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:166870400-166871200	Enhancers	Colon Smooth Muscle	Colon
14	chr1:166870400-166871600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:166870400-166873200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:166870400-166873200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:166870600-166871200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:166870600-166871200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:166870600-166871600	Enhancers	NH-A	brain
20	chr1:166870600-166871800	Enhancers	Fetal Heart	heart
21	chr1:166870600-166872000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:166870600-166873000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:166870800-166871200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:166870800-166871200	Enhancers	Right Atrium	heart

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