Variant report

Variant	rs7628631
Chromosome Location	chr3:47560863-47560864
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	chr3:47559554..47562516-chr3:47592934..47596290,3	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs10865946	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11130132	0.97[EUR][1000 genomes]
rs11130133	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11705957	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11707895	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711824	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs11712445	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11713413	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716763	1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11719877	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11914795	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11914913	0.95[EUR][1000 genomes]
rs11914932	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925823	0.80[EUR][1000 genomes]
rs12486969	0.80[EUR][1000 genomes]
rs12489046	0.91[EUR][1000 genomes]
rs12490058	0.97[EUR][1000 genomes]
rs12492433	0.91[EUR][1000 genomes]
rs12497225	0.81[EUR][1000 genomes]
rs12630641	0.98[EUR][1000 genomes]
rs12632132	0.82[EUR][1000 genomes]
rs12636851	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs13059519	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs13064843	0.81[EUR][1000 genomes]
rs13075233	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1531875	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1564760	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1564761	0.95[ASN][1000 genomes]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs17784882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872164	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1872166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2062278	0.81[EUR][1000 genomes]
rs2101247	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295449	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs295458	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs295461	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs34634681	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3816779	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4599332	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858856	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858868	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs4858894	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs56032309	0.81[EUR][1000 genomes]
rs57346147	0.81[EUR][1000 genomes]
rs59586735	0.91[EUR][1000 genomes]
rs60369822	0.86[EUR][1000 genomes]
rs62248599	0.90[EUR][1000 genomes]
rs62248603	0.86[EUR][1000 genomes]
rs62248605	0.92[EUR][1000 genomes]
rs62260710	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260711	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260741	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765990	0.99[EUR][1000 genomes]
rs6768879	0.88[ASN][1000 genomes]
rs6780013	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs6787422	0.81[EUR][1000 genomes]
rs6790763	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792461	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6792488	0.88[EUR][1000 genomes]
rs6800271	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs73081205	0.89[EUR][1000 genomes]
rs7649234	0.88[EUR][1000 genomes]
rs7651194	0.99[EUR][1000 genomes]
rs7651762	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs878659	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs922957	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9683033	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9683177	0.88[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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7628631	AMIGO3	cis	cerebellum	SCAN
rs7628631	PRKAR2A	cis	cerebellum	SCAN
rs7628631	SCAP	cis	parietal	SCAN
rs7628631	HYAL2	cis	cerebellum	SCAN
rs7628631	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7628631	IFRD2	cis	parietal	SCAN
rs7628631	NCKIPSD	cis	cerebellum	SCAN
rs7628631	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7628631	C3orf75	cis	cerebellum	SCAN
rs7628631	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47555400-47563800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:47555600-47562000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:47555600-47562000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:47555600-47562200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47555600-47562200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:47555600-47563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:47555600-47563800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:47555600-47563800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:47555600-47563800	Weak transcription	NHLF	lung
10	chr3:47555600-47564200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:47555600-47568200	Weak transcription	Right Atrium	heart
12	chr3:47555800-47562600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:47557800-47562000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:47558000-47562000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:47558000-47562000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:47558000-47562200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:47558400-47562600	Weak transcription	HepG2	liver
18	chr3:47560000-47563800	Weak transcription	K562	blood
19	chr3:47560200-47562200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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