Variant report

Variant	rs935378
Chromosome Location	chr2:47109151-47109152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47104590..47107409-chr2:47107469..47109857,2	K562	blood:
2	chr2:47108239..47110514-chr2:47142135..47144424,2	MCF-7	breast:
3	chr2:47102971..47104916-chr2:47106990..47109724,2	K562	blood:
4	chr2:47107200..47110279-chr2:47111432..47113663,3	K562	blood:
5	chr2:46917588..46920626-chr2:47107576..47110678,3	K562	blood:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1992758	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992759	0.85[EUR][1000 genomes]
rs2084193	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2166479	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28534810	0.85[EUR][1000 genomes]
rs4334538	0.84[CEU][hapmap]
rs55725273	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55978204	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58066895	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60519161	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136790	0.91[EUR][1000 genomes]
rs6544934	0.85[EUR][1000 genomes]
rs72806508	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs751204	0.85[JPT][hapmap]
rs753487	0.93[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs7560018	0.81[JPT][hapmap]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs935378	OXER1	cis	cerebellum	SCAN
rs935378	MCFD2	cis	parietal	SCAN
rs935378	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47097400-47116200	Enhancers	NHDF-Ad	bronchial
2	chr2:47105000-47110000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:47105800-47115800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:47106000-47110600	Weak transcription	Gastric	stomach
5	chr2:47106400-47109600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:47106400-47109600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:47106400-47131000	Weak transcription	Esophagus	oesophagus
8	chr2:47106600-47110000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:47106600-47116000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:47107000-47115800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:47107200-47109400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:47107200-47110800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:47107200-47110800	Enhancers	NHLF	lung
14	chr2:47107400-47109600	Enhancers	Fetal Kidney	kidney
15	chr2:47107400-47117000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:47107800-47109600	Enhancers	Hela-S3	cervix
17	chr2:47107800-47110200	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:47107800-47110200	Enhancers	Right Ventricle	heart
19	chr2:47107800-47110200	Enhancers	HUVEC	blood vessel
20	chr2:47107800-47110400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:47107800-47110600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:47107800-47110600	Enhancers	Placenta	Placenta
23	chr2:47107800-47110800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:47107800-47110800	Enhancers	Left Ventricle	heart
25	chr2:47108000-47110000	Enhancers	Colon Smooth Muscle	Colon
26	chr2:47108200-47110200	Enhancers	Fetal Stomach	stomach
27	chr2:47108200-47110200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:47108200-47110200	Flanking Active TSS	A549	lung
29	chr2:47108200-47110400	Enhancers	Fetal Muscle Leg	muscle
30	chr2:47108200-47110400	Enhancers	Ovary	ovary
31	chr2:47108200-47110400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:47108200-47110400	Enhancers	HSMM	muscle
33	chr2:47108200-47110800	Enhancers	Colonic Mucosa	Colon
34	chr2:47108400-47109200	Flanking Active TSS	Osteobl	bone
35	chr2:47108400-47109400	Enhancers	Spleen	Spleen
36	chr2:47108400-47109600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:47108400-47109600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:47108400-47109600	Enhancers	Fetal Lung	lung
39	chr2:47108400-47110000	Enhancers	Adipose Nuclei	Adipose
40	chr2:47108400-47110000	Bivalent Enhancer	HepG2	liver
41	chr2:47108400-47110200	Enhancers	Right Atrium	heart
42	chr2:47108400-47110200	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:47108400-47110600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:47108400-47110600	Enhancers	Fetal Intestine Large	intestine
45	chr2:47108600-47110000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:47108800-47109400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr2:47108800-47109600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:47108800-47109800	Enhancers	HSMMtube	muscle
49	chr2:47108800-47110200	Enhancers	HMEC	breast
50	chr2:47108800-47110400	Enhancers	Fetal Intestine Small	intestine

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