Variant report

Variant	rs5762938
Chromosome Location	chr22:29382386-29382387
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	CEBPB	chr22:29382347-29382833	MCF-7	breast:	n/a	n/a
2	TCF7L2	chr22:29382362-29382673	HEK293	kidney:	n/a	n/a
3	SETDB1	chr22:29381486-29382744	U2OS	brain:	n/a	n/a
4	HDAC2	chr22:29382320-29382712	MCF-7	breast:	n/a	chr22:29382459-29382468
5	GATA2	chr22:29381959-29382516	SH-SY5Y	brain:	n/a	chr22:29382459-29382469 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
6	GATA3	chr22:29382060-29382970	MCF-7	breast:	n/a	chr22:29382459-29382469 chr22:29382459-29382467 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
7	GATA3	chr22:29381973-29382879	MCF-7	breast:	n/a	chr22:29382459-29382469 chr22:29382459-29382467 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
8	GATA3	chr22:29381907-29382629	SH-SY5Y	brain:	n/a	chr22:29382459-29382469 chr22:29382459-29382467 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
9	GATA3	chr22:29382211-29382752	SK-N-SH	brain:	n/a	chr22:29382459-29382469 chr22:29382459-29382467 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
10	GATA3	chr22:29382171-29382819	SK-N-SH	brain:	n/a	chr22:29382459-29382469 chr22:29382459-29382467 chr22:29382292-29382308 chr22:29382458-29382470 chr22:29382460-29382469
11	CEBPB	chr22:29382369-29382885	MCF-7	breast:	n/a	n/a
12	KAP1	chr22:29381708-29382880	U2OS	brain:	n/a	n/a
13	KAP1	chr22:29381453-29382833	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29381053..29382745-chr22:29384377..29385897,2	K562	blood:
2	chr22:29380991..29382745-chr22:29384341..29385877,2	K562	blood:

Variant related genes	Relation type
ZNRF3	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11912198	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16986908	1.00[EUR][1000 genomes]
rs16986912	1.00[EUR][1000 genomes]
rs16986925	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16986971	1.00[EUR][1000 genomes]
rs16986990	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4823000	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs5752840	0.90[JPT][hapmap]
rs5752848	0.86[ASN][1000 genomes]
rs5752850	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762883	1.00[JPT][hapmap]
rs5762922	0.98[ASN][1000 genomes]
rs5762923	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs5762926	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762928	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs5762929	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5762930	0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762931	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762932	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5762944	0.86[ASN][1000 genomes]
rs7287755	0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs8137391	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8140640	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29365800-29394800	Weak transcription	Pancreas	Pancrea
2	chr22:29373400-29390800	Weak transcription	Hela-S3	cervix
3	chr22:29373600-29400200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr22:29374200-29383000	Weak transcription	Ovary	ovary
5	chr22:29374400-29395200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr22:29374600-29385000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr22:29374600-29395600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr22:29374600-29400000	Weak transcription	Right Ventricle	heart
9	chr22:29374600-29401200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr22:29374800-29384400	Weak transcription	Osteobl	bone
11	chr22:29375200-29385200	Weak transcription	Brain Substantia Nigra	brain
12	chr22:29375600-29383000	Weak transcription	Left Ventricle	heart
13	chr22:29375600-29390800	Weak transcription	NHDF-Ad	bronchial
14	chr22:29375800-29383000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr22:29375800-29383200	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:29375800-29383200	Weak transcription	Fetal Intestine Large	intestine
17	chr22:29375800-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:29376600-29383600	Weak transcription	K562	blood
19	chr22:29376600-29384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr22:29378000-29383600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr22:29378000-29385400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:29378800-29384200	Weak transcription	A549	lung
23	chr22:29379000-29383200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr22:29379000-29383400	Enhancers	Adipose Nuclei	Adipose
25	chr22:29379600-29388400	Weak transcription	Psoas Muscle	Psoas
26	chr22:29379600-29400800	Weak transcription	Fetal Brain Female	brain
27	chr22:29379800-29382600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr22:29379800-29383000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr22:29379800-29383000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr22:29379800-29383800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr22:29380000-29383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr22:29380000-29388400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr22:29380400-29382400	Weak transcription	Fetal Lung	lung
34	chr22:29380400-29382800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr22:29380400-29383000	Weak transcription	Gastric	stomach
36	chr22:29380400-29384800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr22:29380600-29384200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:29380800-29382400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29380800-29383200	Weak transcription	Brain Anterior Caudate	brain
40	chr22:29380800-29400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr22:29381000-29382400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:29381000-29383200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr22:29381000-29385200	Genic enhancers	HepG2	liver
44	chr22:29381000-29386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:29381000-29388400	Weak transcription	Fetal Heart	heart
46	chr22:29381000-29393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:29381000-29395600	Weak transcription	Esophagus	oesophagus
48	chr22:29381200-29382400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr22:29381200-29383000	Weak transcription	Right Atrium	heart
50	chr22:29381200-29383200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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