Variant report

Variant	rs300905
Chromosome Location	chr4:144240473-144240474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:144238199..144241165-chr4:144253825..144255392,2	K562	blood:
2	chr4:144228357..144232212-chr4:144238301..144241767,5	K562	blood:
3	chr4:144235945..144238860-chr4:144239571..144241521,2	K562	blood:

Variant related genes	Relation type
ENSG00000200049	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10028909	0.84[AMR][1000 genomes]
rs1027851	0.84[JPT][hapmap]
rs11100788	0.82[JPT][hapmap]
rs11947952	0.93[ASN][1000 genomes]
rs12643013	0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs13118846	0.87[AMR][1000 genomes]
rs13123498	0.84[JPT][hapmap]
rs13129434	0.85[AMR][1000 genomes]
rs13137362	0.80[AMR][1000 genomes]
rs1472873	0.84[JPT][hapmap]
rs1510880	0.84[JPT][hapmap]
rs1532981	0.87[AMR][1000 genomes]
rs2013856	0.90[ASN][1000 genomes]
rs2055730	0.84[JPT][hapmap]
rs300890	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300891	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300892	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300893	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300894	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs300895	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300899	0.93[ASN][1000 genomes]
rs300901	0.96[ASN][1000 genomes]
rs300902	0.94[ASN][1000 genomes]
rs300903	0.97[ASN][1000 genomes]
rs300904	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300910	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs300911	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs300912	0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs300913	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs300914	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs300915	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs300917	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs300918	0.86[ASN][1000 genomes]
rs300919	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs3792652	0.84[JPT][hapmap]
rs3805247	0.84[JPT][hapmap]
rs3805249	0.83[JPT][hapmap]
rs3805251	0.82[JPT][hapmap]
rs3805253	0.84[JPT][hapmap]
rs3805254	0.84[JPT][hapmap]
rs3805256	0.84[JPT][hapmap]
rs3805257	0.84[JPT][hapmap]
rs3828512	0.84[JPT][hapmap]
rs3828513	0.84[JPT][hapmap]
rs568685	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62337488	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624170	0.93[ASN][1000 genomes]
rs624189	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537152	0.85[AMR][1000 genomes]
rs6537153	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6537155	0.84[JPT][hapmap]
rs6823434	0.85[AMR][1000 genomes]
rs6840603	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs713140	0.84[JPT][hapmap]
rs719392	0.84[JPT][hapmap]
rs7655782	0.87[AMR][1000 genomes]
rs7680959	0.84[JPT][hapmap]
rs7690761	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv3332574	chr4:144239396-144259577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs300905	ZNF330	cis	parietal	SCAN
rs300905	SETD7	cis	parietal	SCAN
rs300905	INPP4B	cis	cerebellum	SCAN
rs300905	ELMOD2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144235000-144247000	Weak transcription	Right Atrium	heart
2	chr4:144235600-144241000	Weak transcription	Left Ventricle	heart
3	chr4:144239000-144241000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:144239000-144241200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:144240200-144242800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:144240400-144240600	Enhancers	Brain Substantia Nigra	brain
7	chr4:144240400-144241200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:144240400-144241200	Enhancers	Colon Smooth Muscle	Colon
9	chr4:144240400-144242200	Enhancers	Fetal Heart	heart

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