Variant report

Variant	rs73926978
Chromosome Location	chr2:47161164-47161165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47152236..47154946-chr2:47158648..47161233,3	K562	blood:
2	chr2:47159700..47162383-chr2:47166830..47168688,2	MCF-7	breast:
3	chr2:47160863..47164193-chr2:47400437..47404755,4	K562	blood:
4	chr2:47160386..47162662-chr2:47182843..47185393,2	MCF-7	breast:
5	chr2:47142431..47146258-chr2:47159598..47162357,3	K562	blood:
6	chr2:47141885..47146886-chr2:47158240..47162628,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272814	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10084332	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10164756	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10165085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181411	0.85[AMR][1000 genomes]
rs10186980	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11897050	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13391660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13406024	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13407588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409489	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13417753	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13424086	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13430346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13430703	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035878	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17035912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28405928	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28465613	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28529158	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28612371	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28770495	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4300885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4314044	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4583513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6729569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926979	0.82[AFR][1000 genomes]
rs73926980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926983	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73926986	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926988	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7603884	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9973769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73926978	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
2	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
3	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
4	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:47150600-47166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:47151000-47166800	Weak transcription	Small Intestine	intestine
8	chr2:47153400-47164400	Weak transcription	Thymus	Thymus
9	chr2:47153800-47166600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:47154000-47166400	Weak transcription	Hela-S3	cervix
11	chr2:47154400-47163600	Weak transcription	Osteobl	bone
12	chr2:47154400-47166800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:47155200-47164400	Weak transcription	Fetal Thymus	thymus
14	chr2:47155800-47166600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:47157200-47166600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:47157400-47166600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:47159400-47163000	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:47159800-47161600	Enhancers	Primary B cells from cord blood	blood
19	chr2:47160000-47167200	Weak transcription	Fetal Stomach	stomach
20	chr2:47160400-47162200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:47160600-47162400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:47160600-47166800	Weak transcription	GM12878-XiMat	blood
23	chr2:47161000-47161600	Enhancers	Primary T cells from cord blood	blood
24	chr2:47161000-47161600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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