Variant report

Variant	rs2074312
Chromosome Location	chr11:17421790-17421791
allele	C/T
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	TBL1XR1	chr11:17421667-17421839	GM12878	blood:	n/a	n/a
2	PAX5	chr11:17421664-17421945	GM12878	blood:	n/a	n/a
3	RUNX3	chr11:17421629-17421855	GM12878	blood:	n/a	n/a
4	CTCF	chr11:17421760-17421910	GM12873	blood:	n/a	n/a
5	SPI1	chr11:17421583-17422367	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ABCC8	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1002227	0.80[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10766389	0.81[CEU][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs10766391	0.81[CEU][hapmap]
rs10766392	1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10766393	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs10766396	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10832770	1.00[YRI][hapmap]
rs10832779	0.81[CEU][hapmap];0.88[YRI][hapmap]
rs10832785	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs11024273	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs11024275	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2067043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074313	0.93[EUR][1000 genomes]
rs2285676	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs3741203	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs41282912	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4148638	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5218	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9633836	0.81[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs9645621	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540951	chr11:17404438-17422755	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv540952	chr11:17407913-17422755	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv467713	chr11:17408025-17440473	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv553584	chr11:17408025-17440473	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2074312	TSG101	cis	cerebellum	SCAN
rs2074312	SPTY2D1	cis	parietal	SCAN
rs2074312	LOC494141	cis	lymphoblastoid	seeQTL
rs2074312	ABCC8	cis	cerebellum	SCAN
rs2074312	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs2074312	GTF2H1	cis	parietal	SCAN
rs2074312	KCNJ11	cis	cerebellum	SCAN
rs2074312	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs2074312	GTF2H1	cis	cerebellum	SCAN
rs2074312	SAA4	cis	parietal	SCAN
rs2074312	ABCC8	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17411400-17422600	Weak transcription	Right Atrium	heart
2	chr11:17411800-17426000	Weak transcription	Lung	lung
3	chr11:17411800-17426000	Weak transcription	Pancreas	Pancrea
4	chr11:17411800-17426800	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:17411800-17426800	Weak transcription	Brain Substantia Nigra	brain
6	chr11:17411800-17435000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:17413200-17432400	Weak transcription	Dnd41	blood
8	chr11:17416200-17423800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:17417400-17422800	Weak transcription	Brain Anterior Caudate	brain
10	chr11:17417800-17422600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr11:17417800-17428200	Weak transcription	Gastric	stomach
12	chr11:17418600-17453600	Weak transcription	Fetal Brain Female	brain
13	chr11:17419400-17421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:17419800-17421800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:17420000-17421800	Weak transcription	Brain Angular Gyrus	brain
16	chr11:17420000-17427000	Weak transcription	Brain Germinal Matrix	brain
17	chr11:17420600-17427000	Weak transcription	Hela-S3	cervix
18	chr11:17421000-17423600	Enhancers	Primary B cells from peripheral blood	blood
19	chr11:17421000-17424600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:17421400-17421800	Enhancers	GM12878-XiMat	blood
21	chr11:17421400-17421800	Enhancers	HSMM	muscle
22	chr11:17421400-17423000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr11:17421400-17423400	Enhancers	HSMMtube	muscle
24	chr11:17421600-17421800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:17421600-17422800	Enhancers	Primary B cells from cord blood	blood
26	chr11:17421600-17423600	Enhancers	Fetal Muscle Leg	muscle
27	chr11:17421600-17427000	Enhancers	Skeletal Muscle Female	skeletal muscle

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