Variant report

Variant	rs60194846
Chromosome Location	chr2:47151292-47151293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47141158..47144890-chr2:47149096..47152105,4	K562	blood:
2	chr2:47141943..47144747-chr2:47148275..47152232,4	MCF-7	breast:
3	chr2:47149635..47151373-chr2:47152965..47154617,2	K562	blood:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10190862	0.88[EUR][1000 genomes]
rs10190882	0.88[EUR][1000 genomes]
rs10197474	0.88[EUR][1000 genomes]
rs10199965	0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.96[ASN][1000 genomes]
rs13388612	1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13394007	0.88[EUR][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs13410702	0.88[EUR][1000 genomes]
rs13415655	0.88[EUR][1000 genomes]
rs13415771	0.88[EUR][1000 genomes]
rs13419072	0.88[EUR][1000 genomes]
rs1446499	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446500	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035813	0.81[EUR][1000 genomes]
rs17035823	0.81[EUR][1000 genomes]
rs17035859	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035867	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035884	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035887	0.94[ASN][1000 genomes]
rs2084192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	1.00[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213467	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58589709	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136788	0.88[EUR][1000 genomes]
rs62136818	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136819	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136820	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62136822	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62140556	0.85[AMR][1000 genomes]
rs6544938	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.96[ASN][1000 genomes]
rs6714269	0.81[EUR][1000 genomes]
rs6715391	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715620	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729120	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729604	1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	0.94[ASN][1000 genomes]
rs6743994	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745578	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755303	0.98[ASN][1000 genomes]
rs6758093	1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs71423929	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720827	0.88[EUR][1000 genomes]
rs7340475	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73926966	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754411	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.85[ASN][1000 genomes]
rs7574833	0.83[ASN][1000 genomes]
rs7575172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586004	0.94[ASN][1000 genomes]
rs7596198	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973504	0.90[ASN][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
rs60194846	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47143800-47151800	Weak transcription	Lung	lung
2	chr2:47144200-47151800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:47144200-47153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:47144200-47153200	Weak transcription	Fetal Stomach	stomach
5	chr2:47144200-47153800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:47144200-47154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:47144200-47155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:47144200-47157200	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
10	chr2:47144400-47153000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:47144400-47153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:47144400-47154400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:47144600-47153000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:47144600-47153000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
16	chr2:47144800-47153200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:47144800-47153400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
19	chr2:47145200-47153200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:47145200-47153400	Weak transcription	Fetal Heart	heart
21	chr2:47145800-47153400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:47146200-47153200	Weak transcription	K562	blood
24	chr2:47147000-47153400	Weak transcription	Primary B cells from cord blood	blood
25	chr2:47147200-47153200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:47147200-47153200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:47148200-47152000	Enhancers	Primary T cells from cord blood	blood
28	chr2:47148600-47152800	Enhancers	Fetal Thymus	thymus
29	chr2:47149200-47153000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:47149600-47153600	Enhancers	Dnd41	blood
31	chr2:47149800-47152000	Enhancers	Fetal Intestine Large	intestine
32	chr2:47149800-47152000	Enhancers	Fetal Intestine Small	intestine
33	chr2:47149800-47153400	Enhancers	Thymus	Thymus
34	chr2:47150400-47153200	Weak transcription	NH-A	brain
35	chr2:47150600-47151400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:47150600-47151800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:47150600-47153000	Weak transcription	HMEC	breast
38	chr2:47150600-47153200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:47150600-47153200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:47150600-47156600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:47150600-47166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:47150600-47167000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:47150800-47152600	Enhancers	Placenta	Placenta
44	chr2:47150800-47152800	Weak transcription	Hela-S3	cervix
45	chr2:47150800-47152800	Weak transcription	NHEK	skin
46	chr2:47150800-47153200	Weak transcription	Osteobl	bone
47	chr2:47150800-47157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:47151000-47151400	Weak transcription	HepG2	liver
49	chr2:47151000-47153000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:47151000-47153200	Weak transcription	Duodenum Mucosa	Duodenum

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