Variant report

Variant	rs62306390
Chromosome Location	chr4:90031328-90031329
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	CTCF	chr4:90031316-90031339	LNCaP	prostate:	n/a	n/a
2	RCOR1	chr4:90031193-90031568	K562	blood:	n/a	n/a
3	MXI1	chr4:90030919-90033825	SK-N-SH	brain:	n/a	chr4:90031789-90031804
4	CTCF	chr4:90031311-90033365	A549	lung:	n/a	n/a
5	SETDB1	chr4:90031327-90033996	U2OS	brain:	n/a	n/a
6	MXI1	chr4:90031119-90033780	IMR90	lung:	n/a	chr4:90031789-90031804

No.	Distal block	Cell Line	Cell type
1	chr4:89443831..89446134-chr4:90031080..90033028,2	K562	blood:
2	chr4:89739934..89740458-chr4:90031072..90031943,2	K562	blood:
3	chr4:90021012..90023295-chr4:90030744..90032396,2	K562	blood:
4	chr4:90030188..90033002-chr4:90049823..90052502,2	MCF-7	breast:

Variant related genes	Relation type
TIGD2	TF binding region
ENSG00000271359	TF binding region
ENSG00000138641	Chromatin interaction
ENSG00000212226	Chromatin interaction
ENSG00000145337	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11097208	0.84[AMR][1000 genomes]
rs12640018	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398940	0.82[ASN][1000 genomes]
rs1398944	0.81[EUR][1000 genomes]
rs17015027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015052	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1708668	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1708669	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1708670	0.84[ASN][1000 genomes]
rs1708681	0.86[ASN][1000 genomes]
rs1795722	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1795727	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1795729	0.83[ASN][1000 genomes]
rs1795734	0.82[ASN][1000 genomes]
rs1795738	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1849597	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1921684	0.84[AMR][1000 genomes]
rs1961979	0.84[AMR][1000 genomes]
rs2018779	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2090031	0.89[ASN][1000 genomes]
rs2464514	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670623	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2704571	0.86[ASN][1000 genomes]
rs28600923	0.87[ASN][1000 genomes]
rs28628620	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2869971	0.84[AMR][1000 genomes]
rs2869972	0.84[AMR][1000 genomes]
rs28712360	0.84[AMR][1000 genomes]
rs2904261	0.84[AMR][1000 genomes]
rs4285052	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4450885	0.84[AMR][1000 genomes]
rs59924504	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60618725	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62306363	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62306364	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62306391	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62306397	0.84[AMR][1000 genomes]
rs6821678	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6852373	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6853480	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72877642	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7656238	0.84[AMR][1000 genomes]
rs7658455	0.81[EUR][1000 genomes]
rs7659904	0.84[AMR][1000 genomes]
rs7660314	0.84[AMR][1000 genomes]
rs7680864	0.84[AMR][1000 genomes]
rs7692291	0.81[EUR][1000 genomes]
rs9307061	0.84[AMR][1000 genomes]
rs9991237	0.84[AMR][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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90017200-90031600	Weak transcription	Right Atrium	heart
2	chr4:90024200-90031800	Weak transcription	Aorta	Aorta
3	chr4:90029600-90031600	Weak transcription	Left Ventricle	heart
4	chr4:90030800-90033600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:90031000-90031400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr4:90031000-90031400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:90031000-90031400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:90031000-90031400	Enhancers	Liver	Liver
9	chr4:90031000-90031400	Enhancers	Fetal Brain Male	brain
10	chr4:90031000-90031400	Active TSS	Fetal Kidney	kidney
11	chr4:90031000-90031600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:90031000-90033400	Active TSS	Pancreas	Pancrea
13	chr4:90031200-90031400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:90031200-90031400	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
15	chr4:90031200-90031400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
16	chr4:90031200-90031400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:90031200-90031400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr4:90031200-90031400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:90031200-90031400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:90031200-90031400	Enhancers	Adipose Nuclei	Adipose
21	chr4:90031200-90031400	Enhancers	Brain Angular Gyrus	brain
22	chr4:90031200-90031400	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:90031200-90031400	Enhancers	Brain Hippocampus Middle	brain
24	chr4:90031200-90031400	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:90031200-90031400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr4:90031200-90031400	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr4:90031200-90031400	Bivalent Enhancer	Fetal Lung	lung
28	chr4:90031200-90031400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:90031200-90031600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:90031200-90031600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr4:90031200-90031600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr4:90031200-90031600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr4:90031200-90031600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:90031200-90031600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr4:90031200-90031600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr4:90031200-90031600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:90031200-90031600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:90031200-90031600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr4:90031200-90031600	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr4:90031200-90031600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr4:90031200-90031600	Bivalent Enhancer	Fetal Stomach	stomach
42	chr4:90031200-90031600	Enhancers	Ovary	ovary
43	chr4:90031200-90031600	Enhancers	Right Ventricle	heart
44	chr4:90031200-90031800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:90031200-90031800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr4:90031200-90033000	Active TSS	Fetal Brain Female	brain
47	chr4:90031200-90033200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr4:90031200-90033400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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