Variant report

Variant	rs942496
Chromosome Location	chr6:33788055-33788056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33760837..33764079-chr6:33785814..33788727,4	MCF-7	breast:
2	chr6:33755474..33757041-chr6:33786349..33788983,2	MCF-7	breast:
3	chr6:33764770..33766513-chr6:33787828..33789808,2	K562	blood:
4	chr6:33776830..33783261-chr6:33784291..33788356,6	K562	blood:

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10947436	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs10947446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11751943	0.83[AFR][1000 genomes]
rs1536501	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.83[AFR][1000 genomes]
rs1547668	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1951930	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182658	0.81[YRI][hapmap]
rs2182659	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs2395399	0.84[ASW][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2395401	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs2395447	0.85[AFR][1000 genomes]
rs2395448	0.83[CEU][hapmap]
rs34095360	0.82[ASN][1000 genomes]
rs3957165	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3998115	1.00[JPT][hapmap]
rs4711350	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4713685	0.88[YRI][hapmap]
rs4713687	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713688	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530614	0.84[ASW][hapmap];0.83[CEU][hapmap];0.82[LWK][hapmap]
rs570749	0.81[AFR][1000 genomes]
rs602399	0.84[ASW][hapmap];0.83[CEU][hapmap];0.85[LWK][hapmap]
rs652049	0.84[ASW][hapmap];0.83[CEU][hapmap];0.83[LWK][hapmap]
rs6915136	1.00[JPT][hapmap]
rs751727	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs943463	0.83[CEU][hapmap]
rs943464	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs943472	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs943476	0.83[ASW][hapmap];0.81[YRI][hapmap]
rs9461905	0.83[CEU][hapmap]
rs9469599	0.82[ASN][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	nsv885773	chr6:33778964-33813043	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv885774	chr6:33778964-33840121	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv885775	chr6:33788055-33828178	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs942496	ZNF76	cis	parietal	SCAN
rs942496	LEMD2	cis	cerebellum	SCAN
rs942496	BAK1	cis	lymphoblastoid	seeQTL
rs942496	C6orf125	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33776400-33792400	Weak transcription	Right Atrium	heart
2	chr6:33781800-33792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:33782200-33790600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33782800-33790600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33783800-33788200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:33785400-33788800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:33785400-33790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:33787600-33788800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:33787600-33790000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:33788000-33788400	Enhancers	Brain Cingulate Gyrus	brain

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