Variant report

Variant	rs11751844
Chromosome Location	chr6:36804661-36804662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36803997..36809047-chr6:36852852..36856509,4	K562	blood:
2	chr6:36802135..36806247-chr6:36814930..36817365,4	K562	blood:
3	chr6:36804125..36807562-chr6:36952553..36955386,3	K562	blood:
4	chr6:36803679..36805737-chr6:36818259..36820032,3	K562	blood:
5	chr6:36804125..36806992-chr6:36952553..36954934,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11751790	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11754437	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11756425	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11758600	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11758807	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12661551	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2007290	0.84[CEU][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs2071822	0.82[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2071823	0.82[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2293381	1.00[YRI][hapmap]
rs236381	0.84[CEU][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs28656041	0.83[ASN][1000 genomes]
rs28673271	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3176344	1.00[YRI][hapmap]
rs3213536	1.00[YRI][hapmap]
rs4711470	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711472	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4714015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714019	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60097056	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62406642	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62406644	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6910582	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6912602	0.84[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs6913047	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72846083	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7745099	0.85[GIH][hapmap]
rs9349015	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9368961	0.83[ASN][1000 genomes]
rs9368963	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368965	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9380603	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs9380605	0.89[JPT][hapmap]
rs9380607	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380614	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9394387	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11751844	TCP11	cis	cerebellum	SCAN
rs11751844	SCUBE3	cis	parietal	SCAN
rs11751844	C6orf125	cis	parietal	SCAN
rs11751844	MAPK13	cis	lymphoblastoid	seeQTL
rs11751844	LRFN2	cis	cerebellum	SCAN
rs11751844	C6orf89	cis	cerebellum	SCAN
rs11751844	C6orf89	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36791200-36805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:36798600-36805400	Weak transcription	Right Ventricle	heart
3	chr6:36798600-36805400	Weak transcription	HUVEC	blood vessel
4	chr6:36798600-36806800	Weak transcription	Ovary	ovary
5	chr6:36798800-36805600	Weak transcription	Right Atrium	heart
6	chr6:36801000-36805000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:36802200-36804800	Enhancers	Fetal Thymus	thymus
8	chr6:36802200-36806400	Enhancers	Fetal Heart	heart
9	chr6:36803000-36805800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:36803000-36806000	Weak transcription	Left Ventricle	heart
11	chr6:36803000-36806400	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:36803200-36806000	Weak transcription	Fetal Brain Female	brain
13	chr6:36803200-36806400	Weak transcription	Fetal Brain Male	brain
14	chr6:36803200-36806600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:36803400-36806200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:36803800-36806600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr6:36804000-36807000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:36804000-36808200	Active TSS	Brain Anterior Caudate	brain
19	chr6:36804200-36805400	Bivalent Enhancer	HepG2	liver
20	chr6:36804600-36804800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr6:36804600-36806000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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