Variant report

Variant	rs4953431
Chromosome Location	chr2:47088920-47088921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47080558..47082163-chr2:47086057..47089027,2	K562	blood:
2	chr2:47087833..47089344-chr2:47097386..47099191,2	MCF-7	breast:
3	chr2:47084849..47086981-chr2:47087555..47090038,3	K562	blood:
4	chr2:47088613..47092145-chr2:47092514..47095025,5	K562	blood:

Variant related genes	Relation type
ENSG00000226548	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11125098	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs13415138	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs4953434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61542554	0.91[EUR][1000 genomes]
rs72804479	0.90[EUR][1000 genomes]
rs875343	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs935380	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv961405	chr2:47088519-47089305	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv979000	chr2:47088519-47093944	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4953431	MCFD2	cis	cerebellum	SCAN
rs4953431	MCFD2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47080800-47103600	Enhancers	Placenta	Placenta
2	chr2:47081400-47091000	Enhancers	NHDF-Ad	bronchial
3	chr2:47082200-47089000	Weak transcription	Colonic Mucosa	Colon
4	chr2:47084000-47093200	Weak transcription	Ovary	ovary
5	chr2:47084000-47093600	Weak transcription	Right Atrium	heart
6	chr2:47085000-47090400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:47085800-47089400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:47086000-47091200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:47086200-47089400	Weak transcription	A549	lung
10	chr2:47086800-47090400	Weak transcription	HSMMtube	muscle
11	chr2:47087200-47089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:47087200-47089200	Weak transcription	NHLF	lung
13	chr2:47087600-47091600	Enhancers	Fetal Lung	lung
14	chr2:47087800-47097400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:47088200-47089400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:47088200-47089400	Bivalent Enhancer	Fetal Stomach	stomach
17	chr2:47088400-47089000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:47088400-47089200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:47088400-47090200	Enhancers	Left Ventricle	heart
20	chr2:47088400-47091400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:47088600-47090000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:47088600-47090200	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:47088600-47090600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:47088600-47092000	Enhancers	Fetal Muscle Leg	muscle
25	chr2:47088800-47089000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr2:47088800-47089400	Enhancers	Adipose Nuclei	Adipose
27	chr2:47088800-47089600	Enhancers	Right Ventricle	heart
28	chr2:47088800-47089800	Enhancers	Colon Smooth Muscle	Colon
29	chr2:47088800-47089800	Enhancers	Fetal Kidney	kidney
30	chr2:47088800-47089800	Enhancers	Fetal Muscle Trunk	muscle
31	chr2:47088800-47090000	Enhancers	Osteobl	bone
32	chr2:47088800-47090400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:47088800-47091200	Weak transcription	Spleen	Spleen
34	chr2:47088800-47091400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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