Variant report

Variant	rs9403826
Chromosome Location	chr6:147218932-147218933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147217369..147219463-chr6:147527173..147529417,2	K562	blood:
2	chr6:147218917..147220717-chr6:147520720..147523033,2	K562	blood:
3	chr6:147217791..147220751-chr6:147534803..147537147,3	K562	blood:
4	chr6:147218209..147220356-chr6:147630497..147633401,2	K562	blood:
5	chr6:147217069..147220905-chr6:147535647..147540121,4	K562	blood:
6	chr6:147218096..147220115-chr6:147523787..147525922,3	K562	blood:

Variant related genes	Relation type
ENSG00000164506	Chromatin interaction
ENSG00000233452	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1022877	0.81[CHD][hapmap]
rs1119876	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1122570	0.83[GIH][hapmap]
rs1324683	0.90[ASN][1000 genomes]
rs1324684	0.81[CHD][hapmap]
rs1324685	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1408575	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1853696	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1924691	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs1924693	0.92[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2224906	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2328769	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs2328770	0.90[JPT][hapmap]
rs259371	0.81[JPT][hapmap]
rs6570778	0.90[JPT][hapmap]
rs6915391	0.90[JPT][hapmap]
rs6926192	0.82[ASN][1000 genomes]
rs6929209	0.90[JPT][hapmap]
rs7740261	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7751561	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755795	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs7766908	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs927672	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9377033	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9377034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386175	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390437	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9390438	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399587	0.90[JPT][hapmap]
rs9403827	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv442012	chr6:147210681-147219817	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9403826	KATNA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147215000-147219200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:147215200-147219600	Flanking Active TSS	K562	blood
3	chr6:147215200-147224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:147216000-147224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:147216800-147220000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:147217000-147220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:147217000-147220400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:147217400-147220600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:147218000-147225800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:147218200-147226600	Weak transcription	NHLF	lung

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