Variant report

Variant	rs9608941
Chromosome Location	chr22:30886886-30886887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:30886831-30886901	GM20000	blood:	n/a	n/a
2	CTCF	chr22:30886820-30886970	HEEpiC	esophagus:	n/a	n/a
3	CTCF	chr22:30886820-30886970	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30885075..30887200-chr22:30887226..30889669,2	MCF-7	breast:
2	chr22:30884994..30887609-chr22:30891940..30894368,2	K562	blood:

Variant related genes	Relation type
ENSG00000181123	TF binding region
ENSG00000181123	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1001409	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11912737	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11914168	1.00[JPT][hapmap]
rs12484688	1.00[JPT][hapmap]
rs13053262	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054004	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054381	0.80[EUR][1000 genomes]
rs13750	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988720	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16988803	1.00[JPT][hapmap]
rs16988810	1.00[JPT][hapmap]
rs16988814	1.00[JPT][hapmap]
rs17670707	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738527	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738540	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[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859479	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1986969	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2023967	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2189835	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412989	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2412990	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35102600	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35530794	1.00[ASN][1000 genomes]
rs35841307	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602314	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820019	1.00[JPT][hapmap]
rs4820856	1.00[YRI][hapmap]
rs4820869	1.00[JPT][hapmap]
rs4820874	1.00[JPT][hapmap]
rs60308761	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518693	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6518695	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7284873	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285878	1.00[ASN][1000 genomes]
rs7286523	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286807	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287003	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287135	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7287596	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7287943	0.96[EUR][1000 genomes]
rs7289277	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289828	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291870	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7292573	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737940	0.80[EUR][1000 genomes]
rs737942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136225	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8136992	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8137267	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8137718	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138759	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[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141108	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141286	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141318	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141428	1.00[ASN][1000 genomes]
rs8141671	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886615	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs886616	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs886617	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9306262	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606739	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606744	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606745	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606746	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606747	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606749	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608935	1.00[ASN][1000 genomes]
rs9608936	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608938	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9608940	1.00[ASN][1000 genomes]
rs9608942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608946	0.97[EUR][1000 genomes]
rs9608955	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs9608960	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608964	1.00[ASN][1000 genomes]
rs9608966	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608967	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608968	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608972	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9608941	NEFH	cis	lymphoblastoid	seeQTL
rs9608941	SEC14L4	cis	lung	GTEx
rs9608941	DUSP18	cis	parietal	SCAN
rs9608941	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30874600-30894000	Weak transcription	Right Atrium	heart
2	chr22:30881800-30890000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:30882000-30888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:30882000-30889400	Weak transcription	Spleen	Spleen
5	chr22:30883400-30901200	Weak transcription	A549	lung
6	chr22:30884800-30891200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:30886200-30887000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:30886400-30893600	Weak transcription	Lung	lung
9	chr22:30886600-30887000	Enhancers	K562	blood
10	chr22:30886600-30892000	Strong transcription	Liver	Liver

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