Variant report

Variant	rs11824940
Chromosome Location	chr11:59826857-59826858
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	FOS	chr11:59826529-59826883	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
2	FOS	chr11:59826552-59826883	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
3	FOS	chr11:59826542-59826896	MCF10A-Er-Src	breast:	n/a	chr11:59826710-59826721
4	EGR1	chr11:59826595-59826860	K562	blood:	n/a	n/a
5	JUND	chr11:59826542-59826927	K562	blood:	n/a	chr11:59826710-59826721
6	JUN	chr11:59826001-59827014	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59822049..59824288-chr11:59826581..59828945,2	K562	blood:

Variant related genes	Relation type
MS4A3	TF binding region
ENSG00000149516	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10792255	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10897003	0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs10897006	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10897007	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11821744	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825794	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12221875	0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs12419784	0.82[YRI][hapmap]
rs12800461	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12805696	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806720	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17154511	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154527	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298584	0.81[AMR][1000 genomes]
rs35691621	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57170676	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7102260	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7106518	0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs7108307	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7109174	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7113196	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11824940	GTF2IRD1	trans	parietal	SCAN
rs11824940	CTNND1	cis	parietal	SCAN
rs11824940	SERPING1	cis	cerebellum	SCAN
rs11824940	TIMM10	cis	cerebellum	SCAN
rs11824940	SLC43A1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59822800-59832000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:59824600-59830000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59825000-59827000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr11:59826400-59828400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:59826600-59829600	Weak transcription	K562	blood

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