Variant report

Variant	rs9405281
Chromosome Location	chr6:5701541-5701542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5692733..5695686-chr6:5700140..5701743,2	K562	blood:
2	chr6:5693144..5695686-chr6:5698907..5701640,2	K562	blood:

Variant related genes	Relation type
ENSG00000270174	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1001568	0.89[CHB][hapmap]
rs11752777	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs13213128	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs2005970	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2142738	0.95[CHB][hapmap]
rs2326634	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4959347	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4960125	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4960126	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62408067	0.81[EUR][1000 genomes]
rs6918561	0.85[CHB][hapmap]
rs6918675	0.85[CHB][hapmap]
rs760675	0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7739358	0.84[JPT][hapmap]
rs7746913	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs877010	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs9328328	0.88[CHB][hapmap]
rs9378979	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs9378980	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs9378983	0.85[CHB][hapmap]
rs9392709	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392710	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405280	0.82[ASN][1000 genomes]
rs9405859	0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs9405861	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9504488	0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3473790	chr6:5692573-5707035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3473791	chr6:5692573-5707035	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv823407	chr6:5692735-5706712	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv970203	chr6:5701414-5703106	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9405281	NQO2	cis	parietal	SCAN
rs9405281	C6orf146	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
4	chr6:5684800-5706000	Weak transcription	Ovary	ovary
5	chr6:5695800-5709800	Weak transcription	Fetal Stomach	stomach
6	chr6:5696200-5707600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:5696200-5712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:5696400-5705400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:5699200-5705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:5699400-5708000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:5699400-5713200	Weak transcription	Esophagus	oesophagus
12	chr6:5699600-5704000	Weak transcription	Lung	lung
13	chr6:5699600-5704800	Weak transcription	Dnd41	blood
14	chr6:5699800-5702000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:5699800-5715800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:5700000-5705600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:5700400-5708200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:5700800-5701800	Enhancers	Spleen	Spleen
19	chr6:5700800-5702200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:5700800-5704200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:5701200-5701600	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:5701200-5701800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:5701200-5702000	Enhancers	Fetal Heart	heart
24	chr6:5701400-5701600	ZNF genes & repeats	Aorta	Aorta
25	chr6:5701400-5701600	Enhancers	Right Atrium	heart
26	chr6:5701400-5702200	Enhancers	Fetal Thymus	thymus

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