Variant report

Variant	rs2082562
Chromosome Location	chr2:47214636-47214637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47213870..47217482-chr2:47217996..47221953,5	MCF-7	breast:
2	chr2:47214296..47216240-chr2:47260136..47264108,3	MCF-7	breast:
3	chr2:47212569..47215623-chr2:47548901..47551029,3	K562	blood:
4	chr2:47213873..47215501-chr2:47549847..47551396,20	K562	blood:
5	chr2:47214073..47216296-chr2:47255513..47257887,2	MCF-7	breast:
6	chr2:47206562..47208636-chr2:47212925..47215220,2	K562	blood:
7	chr2:47213500..47216240-chr2:47548901..47552350,5	K562	blood:
8	chr2:47141714..47144704-chr2:47213169..47216343,3	MCF-7	breast:
9	chr2:47166662..47168239-chr2:47214409..47216366,2	MCF-7	breast:
10	chr2:47211199..47217347-chr2:47399008..47404700,12	K562	blood:
11	chr2:47214279..47216434-chr2:47222625..47224948,2	MCF-7	breast:
12	chr2:47213903..47214786-chr2:47396818..47397476,2	MCF-7	breast:
13	chr2:47146090..47146882-chr2:47213985..47214715,2	MCF-7	breast:
14	chr2:47213608..47215277-chr2:47549985..47550910,10	MCF-7	breast:
15	chr2:47205847..47208964-chr2:47212925..47215633,5	K562	blood:
16	chr2:47214133..47214774-chr2:47499196..47500160,4	K562	blood:
17	chr2:47214252..47214763-chr2:47524847..47525691,2	K562	blood:
18	chr2:47141281..47143622-chr2:47212443..47214863,2	MCF-7	breast:
19	chr2:47168191..47171177-chr2:47214556..47217322,3	MCF-7	breast:
20	chr2:47213985..47214817-chr2:47255980..47256485,2	MCF-7	breast:
21	chr2:47209205..47217024-chr2:47399516..47404811,13	MCF-7	breast:
22	chr2:47214206..47214770-chr20:53290236..53290902,2	MCF-7	breast:
23	chr2:47212859..47216615-chr2:47301507..47304672,4	MCF-7	breast:
24	chr2:47213696..47215367-chr2:47239730..47241544,2	MCF-7	breast:
25	chr2:47213933..47214713-chr2:47539627..47540579,3	MCF-7	breast:
26	chr2:47213989..47214766-chr2:47546474..47547462,2	MCF-7	breast:
27	chr2:47164097..47165002-chr2:47213891..47214776,2	MCF-7	breast:
28	chr2:47187898..47188405-chr2:47213880..47214767,2	K562	blood:
29	chr2:47214614..47216991-chr2:47391312..47393709,3	K562	blood:
30	chr2:47212899..47215171-chr2:47549795..47551134,10	MCF-7	breast:
31	chr2:47211854..47216258-chr2:47229137..47232912,5	K562	blood:
32	chr2:47212912..47216047-chr2:47549012..47553411,7	MCF-7	breast:
33	chr2:47210303..47217706-chr2:47402135..47406405,13	MCF-7	breast:
34	chr2:47214273..47214840-chr2:47276289..47276999,3	K562	blood:
35	chr2:47213957..47214845-chr2:47348299..47348953,3	MCF-7	breast:
36	chr2:47214229..47214810-chr2:47548565..47549556,2	MCF-7	breast:
37	chr2:47212292..47217234-chr2:47401238..47405508,6	K562	blood:
38	chr2:47213916..47214788-chr2:47499094..47500691,5	MCF-7	breast:
39	chr2:47213839..47216114-chr2:47390613..47392812,2	K562	blood:

No data

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

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11125110	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12621059	0.80[YRI][hapmap]
rs4953439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419615	0.89[YRI][hapmap]
rs6753628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736377	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv581750	chr2:47207665-47229953	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2082562	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47196600-47227800	Strong transcription	Dnd41	blood
2	chr2:47200800-47216400	Genic enhancers	Fetal Thymus	thymus
3	chr2:47202000-47214800	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:47208000-47217400	Enhancers	Stomach Mucosa	stomach
5	chr2:47208400-47214800	Enhancers	HUVEC	blood vessel
6	chr2:47208600-47216000	Enhancers	Brain Substantia Nigra	brain
7	chr2:47208600-47219200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:47209400-47217200	Genic enhancers	NHLF	lung
9	chr2:47209600-47215200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:47209600-47217400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:47209600-47218200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:47209800-47214800	Enhancers	Primary hematopoietic stem cells	blood
13	chr2:47210000-47215200	Enhancers	Brain Anterior Caudate	brain
14	chr2:47210200-47215200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:47210200-47215800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr2:47210400-47214800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:47210600-47215600	Weak transcription	Psoas Muscle	Psoas
18	chr2:47210600-47215600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:47210600-47216600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr2:47210800-47215800	Enhancers	Spleen	Spleen
21	chr2:47211000-47214800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:47211000-47215800	Enhancers	Brain Hippocampus Middle	brain
23	chr2:47211400-47214800	Genic enhancers	Osteobl	bone
24	chr2:47211400-47215600	Enhancers	Esophagus	oesophagus
25	chr2:47211400-47217600	Enhancers	Right Atrium	heart
26	chr2:47211600-47214800	Enhancers	HMEC	breast
27	chr2:47211800-47215600	Enhancers	Colonic Mucosa	Colon
28	chr2:47211800-47215800	Enhancers	HSMMtube	muscle
29	chr2:47211800-47218000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:47211800-47218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:47212000-47214800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:47212000-47215000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:47212000-47217200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:47212000-47217200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:47212000-47217600	Enhancers	Rectal Smooth Muscle	rectum
36	chr2:47212200-47214800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:47212200-47218200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:47212400-47214800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:47212400-47215600	Enhancers	NHDF-Ad	bronchial
40	chr2:47212400-47217000	Enhancers	Fetal Heart	heart
41	chr2:47212400-47217600	Enhancers	Fetal Muscle Trunk	muscle
42	chr2:47212600-47214800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:47212600-47214800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:47212600-47217400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:47212800-47214800	Enhancers	Placenta	Placenta
46	chr2:47212800-47214800	Enhancers	NH-A	brain
47	chr2:47212800-47215200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:47212800-47215600	Enhancers	Adipose Nuclei	Adipose
49	chr2:47212800-47217400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:47213000-47214800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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