Variant report

Variant	rs2444898
Chromosome Location	chr8:99027677-99027678
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	REST	chr8:99027594-99027883	SK-N-SH	brain:	n/a	n/a
2	ELF1	chr8:99027639-99027932	K562	blood:	n/a	chr8:99027802-99027815
3	GATA2	chr8:99027391-99028036	SH-SY5Y	brain:	n/a	n/a
4	MAFK	chr8:99027622-99027813	HepG2	liver:	n/a	n/a
5	TCF7L2	chr8:99027358-99027808	Hela-S3	cervix:	n/a	n/a
6	EP300	chr8:99027569-99027968	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr8:99027581-99027968	SK-N-SH	brain:	n/a	n/a
8	EP300	chr8:99027576-99028007	SK-N-SH_RA	brain:	n/a	n/a
9	PBX3	chr8:99027664-99028064	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr8:99027498-99028183	SK-N-SH	brain:	n/a	n/a
11	EP300	chr8:99027262-99028234	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99024327..99027909-chr8:99029199..99033016,4	MCF-7	breast:
2	chr8:99026660..99028178-chr8:99029956..99031534,2	MCF-7	breast:

Variant related genes	Relation type
MATN2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10088117	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10093417	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12334735	0.85[AFR][1000 genomes]
rs13439751	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs1378122	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454713	0.88[JPT][hapmap]
rs2010016	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061052	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331692	0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2444857	0.83[JPT][hapmap]
rs2444859	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2444866	0.89[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs2444885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2444894	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2447488	0.83[ASN][1000 genomes]
rs2513806	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2513808	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513815	0.94[ASN][1000 genomes]
rs2513817	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs2513819	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2513823	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2959642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73701228	0.85[AFR][1000 genomes]
rs748324	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
2	chr8:99009000-99030000	Weak transcription	Pancreas	Pancrea
3	chr8:99009000-99030200	Weak transcription	Esophagus	oesophagus
4	chr8:99012000-99028800	Weak transcription	Aorta	Aorta
5	chr8:99012000-99032000	Weak transcription	Gastric	stomach
6	chr8:99012400-99028800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr8:99014200-99029600	Weak transcription	Fetal Intestine Large	intestine
8	chr8:99015000-99034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:99019000-99033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr8:99020000-99033400	Weak transcription	Left Ventricle	heart
11	chr8:99021000-99028600	Weak transcription	Liver	Liver
12	chr8:99021000-99032200	Weak transcription	Brain Substantia Nigra	brain
13	chr8:99021200-99032800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:99021200-99053600	Weak transcription	A549	lung
15	chr8:99021400-99029400	Weak transcription	Brain Angular Gyrus	brain
16	chr8:99021400-99029600	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:99021400-99029800	Weak transcription	Brain Anterior Caudate	brain
18	chr8:99021400-99029800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr8:99021400-99033400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:99021400-99043800	Weak transcription	Brain Germinal Matrix	brain
21	chr8:99021600-99028800	Weak transcription	Adipose Nuclei	Adipose
22	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr8:99023000-99033400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:99023200-99030000	Weak transcription	Fetal Intestine Small	intestine
25	chr8:99023600-99034800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr8:99023800-99041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:99024000-99030000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr8:99024000-99030000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr8:99024000-99030200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:99024000-99032800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:99024000-99044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
33	chr8:99024200-99028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:99024200-99030000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:99024200-99032800	Weak transcription	Colon Smooth Muscle	Colon
36	chr8:99024200-99033200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:99024200-99033200	Weak transcription	NHDF-Ad	bronchial
38	chr8:99024200-99033600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr8:99024200-99042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
41	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
42	chr8:99024400-99029800	Weak transcription	Fetal Kidney	kidney
43	chr8:99024400-99032800	Weak transcription	HSMMtube	muscle
44	chr8:99024600-99028800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr8:99024600-99028800	Weak transcription	Osteobl	bone
46	chr8:99024600-99030000	Weak transcription	Fetal Lung	lung
47	chr8:99025000-99030600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr8:99025000-99052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:99025200-99030000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr8:99025200-99030000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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