Variant report

Variant	rs5752867
Chromosome Location	chr22:29513729-29513730
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	chr22:29513716-29514643	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
KREMEN1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs126077	0.93[GIH][hapmap];0.83[TSI][hapmap]
rs134591	0.81[TSI][hapmap]
rs134651	0.83[TSI][hapmap]
rs134656	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134657	0.83[YRI][hapmap]
rs134665	0.81[TSI][hapmap]
rs134667	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134669	0.83[YRI][hapmap]
rs134672	0.82[YRI][hapmap]
rs134674	0.88[CEU][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134676	0.83[YRI][hapmap]
rs134677	0.83[YRI][hapmap]
rs134678	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs134688	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs134689	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs2157394	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2881801	0.82[ASN][1000 genomes]
rs4330194	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4330195	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820795	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823011	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823012	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823013	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823014	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762992	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762994	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs739210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5752867	ZNRF3	cis	cerebellum	SCAN
rs5752867	SLC35E4	cis	cerebellum	SCAN
rs5752867	TBC1D10A	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29483400-29550200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr22:29486600-29519000	Weak transcription	Fetal Brain Male	brain
3	chr22:29488400-29521200	Weak transcription	Lung	lung
4	chr22:29490000-29514000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:29490400-29539800	Weak transcription	Psoas Muscle	Psoas
6	chr22:29491200-29521200	Weak transcription	Colonic Mucosa	Colon
7	chr22:29491600-29522200	Weak transcription	Liver	Liver
8	chr22:29493200-29521000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr22:29493200-29521200	Weak transcription	Pancreas	Pancrea
10	chr22:29493200-29536400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:29493400-29516400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr22:29495200-29516600	Weak transcription	Esophagus	oesophagus
13	chr22:29504800-29521800	Weak transcription	NHEK	skin
14	chr22:29505000-29514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:29505000-29521000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr22:29505800-29533000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:29506000-29514000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr22:29506000-29521000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr22:29506400-29513800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:29506400-29514000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:29506400-29516200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr22:29506400-29516400	Weak transcription	Adipose Nuclei	Adipose
23	chr22:29506400-29516400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr22:29506400-29520000	Weak transcription	Fetal Thymus	thymus
25	chr22:29506400-29521000	Weak transcription	Right Ventricle	heart
26	chr22:29506400-29522200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:29506400-29522400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr22:29506600-29514000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr22:29507000-29520200	Weak transcription	Thymus	Thymus
30	chr22:29508200-29537200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr22:29509000-29514000	Weak transcription	Placenta	Placenta
32	chr22:29509400-29524400	Weak transcription	NHDF-Ad	bronchial
33	chr22:29509400-29525000	Weak transcription	Osteobl	bone
34	chr22:29509600-29513800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:29509800-29516400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:29510000-29516200	Weak transcription	Brain Angular Gyrus	brain
37	chr22:29510000-29516400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr22:29510000-29519800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr22:29510000-29525400	Weak transcription	Brain Anterior Caudate	brain
40	chr22:29510000-29528200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:29510000-29530800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr22:29510000-29531000	Weak transcription	Brain Hippocampus Middle	brain
43	chr22:29510200-29514400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:29510200-29521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:29510200-29531000	Weak transcription	Brain Substantia Nigra	brain
46	chr22:29510800-29514400	Enhancers	HepG2	liver
47	chr22:29511400-29513800	Enhancers	Fetal Stomach	stomach
48	chr22:29512000-29514600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr22:29512200-29514400	ZNF genes & repeats	Dnd41	blood
50	chr22:29512400-29514000	Weak transcription	Left Ventricle	heart

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