Variant report

Variant	rs12621059
Chromosome Location	chr2:47149658-47149659
allele	C/T
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	chr2:47148104..47150169-chr2:47400944..47403162,2	K562	blood:
4	chr2:47149635..47151373-chr2:47152965..47154617,2	K562	blood:
5	chr2:47147988..47149803-chr2:47547062..47549076,2	MCF-7	breast:

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

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1051317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2082562	0.80[YRI][hapmap]
rs2117168	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140549	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6419615	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544941	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6753628	0.80[YRI][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
rs12621059	STON1-GTF2A1L	cis	parietal	SCAN
rs12621059	MCFD2	cis	parietal	SCAN
rs12621059	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47143800-47151800	Weak transcription	Lung	lung
2	chr2:47144000-47150800	Weak transcription	Placenta	Placenta
3	chr2:47144200-47149800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:47144200-47150000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:47144200-47150200	Weak transcription	Gastric	stomach
6	chr2:47144200-47151800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:47144200-47153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:47144200-47153200	Weak transcription	Fetal Stomach	stomach
9	chr2:47144200-47153800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:47144200-47154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:47144200-47155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:47144200-47157200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
14	chr2:47144400-47153000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:47144400-47153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:47144400-47154400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:47144600-47149800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:47144600-47149800	Weak transcription	Fetal Intestine Small	intestine
19	chr2:47144600-47149800	Weak transcription	HMEC	breast
20	chr2:47144600-47153000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:47144600-47153000	Weak transcription	Brain Germinal Matrix	brain
22	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
23	chr2:47144800-47149800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:47144800-47150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:47144800-47153200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:47144800-47153400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:47144800-47167000	Weak transcription	Fetal Lung	lung
28	chr2:47145000-47150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:47145200-47150200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:47145200-47150400	Weak transcription	Hela-S3	cervix
31	chr2:47145200-47153200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:47145200-47153400	Weak transcription	Fetal Heart	heart
33	chr2:47145800-47153400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:47146000-47150000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:47146000-47150000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:47146000-47150200	Weak transcription	NHLF	lung
37	chr2:47146000-47167400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:47146200-47150000	Weak transcription	HepG2	liver
39	chr2:47146200-47150800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:47146200-47153200	Weak transcription	K562	blood
41	chr2:47147000-47153400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:47147200-47153200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:47147200-47153200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:47148200-47152000	Enhancers	Primary T cells from cord blood	blood
45	chr2:47148400-47150600	Enhancers	HUVEC	blood vessel
46	chr2:47148600-47152800	Enhancers	Fetal Thymus	thymus
47	chr2:47148800-47150400	Enhancers	NH-A	brain
48	chr2:47148800-47150600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr2:47148800-47150800	Enhancers	Osteobl	bone
50	chr2:47149000-47150200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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