Variant report

Variant	rs6882940
Chromosome Location	chr5:179648989-179648990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179640079..179643387-chr5:179646560..179650820,4	K562	blood:
2	chr5:179647507..179649585-chr5:179676137..179678589,2	K562	blood:
3	chr5:179646664..179649046-chr5:179651579..179654068,2	K562	blood:

Variant related genes	Relation type
ENSG00000229721	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10155559	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10903250	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1127580	0.82[EUR][1000 genomes]
rs17627536	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17627815	0.94[CEU][hapmap]
rs17627880	0.95[CEU][hapmap]
rs3099063	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs3111536	0.85[EUR][1000 genomes]
rs34763496	0.83[EUR][1000 genomes]
rs35211991	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35394934	0.85[EUR][1000 genomes]
rs35551113	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35759987	0.85[EUR][1000 genomes]
rs4270655	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4273568	0.89[YRI][hapmap]
rs4309929	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4454029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4469167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700728	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55756747	0.85[EUR][1000 genomes]
rs56929977	0.86[ASN][1000 genomes]
rs62406982	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62406984	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62406986	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406991	0.85[EUR][1000 genomes]
rs6703	0.82[CEU][hapmap]
rs6864789	0.82[ASN][1000 genomes]
rs6867398	0.91[GIH][hapmap]
rs6869231	0.87[EUR][1000 genomes]
rs6874557	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6877489	0.86[CEU][hapmap]
rs6878432	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6894217	0.83[EUR][1000 genomes]
rs7708873	0.85[CEU][hapmap]
rs7722861	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
2	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
4	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6882940	MAPK9	cis	cerebellum	SCAN
rs6882940	RASGEF1C	cis	parietal	SCAN
rs6882940	FLT4	cis	cerebellum	SCAN
rs6882940	MAPK9	cis	multi-tissue	Pritchard
rs6882940	MAPK9	cis	lymphoblastoid	seeQTL
rs6882940	ZNF346	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179645600-179660200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:179646800-179659200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:179647400-179650200	ZNF genes & repeats	Liver	Liver
4	chr5:179647600-179659800	Weak transcription	Brain Angular Gyrus	brain
5	chr5:179647600-179660200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:179647800-179656600	Weak transcription	Brain Anterior Caudate	brain
7	chr5:179648800-179649400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:179648800-179649600	ZNF genes & repeats	Gastric	stomach

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