Variant report

Variant	rs6715391
Chromosome Location	chr2:47130678-47130679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47130325..47132416-chr2:47141397..47144318,2	MCF-7	breast:
2	chr2:47127542..47131326-chr2:47131677..47134825,5	K562	blood:
3	chr2:47127713..47130924-chr2:47141446..47144583,3	MCF-7	breast:
4	chr2:47114369..47117073-chr2:47127351..47131177,3	K562	blood:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10174894	0.94[ASN][1000 genomes]
rs10190862	0.94[EUR][1000 genomes]
rs10190882	0.94[EUR][1000 genomes]
rs10197474	0.94[EUR][1000 genomes]
rs10199965	1.00[ASN][1000 genomes]
rs11890177	1.00[ASN][1000 genomes]
rs11894319	0.94[ASN][1000 genomes]
rs13388612	0.94[ASN][1000 genomes]
rs13392448	0.89[ASN][1000 genomes]
rs13394007	0.94[EUR][1000 genomes]
rs13398851	0.85[ASN][1000 genomes]
rs13410702	0.94[EUR][1000 genomes]
rs13415655	0.94[EUR][1000 genomes]
rs13415771	0.94[EUR][1000 genomes]
rs13419072	0.94[EUR][1000 genomes]
rs1446499	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1446500	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17035859	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17035867	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035884	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035887	1.00[ASN][1000 genomes]
rs2084192	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289927	0.94[ASN][1000 genomes]
rs2289928	0.94[ASN][1000 genomes]
rs2347259	0.94[ASN][1000 genomes]
rs28516550	1.00[ASN][1000 genomes]
rs3087857	0.94[ASN][1000 genomes]
rs34581142	0.94[ASN][1000 genomes]
rs35433380	0.94[ASN][1000 genomes]
rs4505575	0.86[ASN][1000 genomes]
rs55872217	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56213467	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58589709	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60194846	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61132855	0.94[ASN][1000 genomes]
rs62136788	0.94[EUR][1000 genomes]
rs62136818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62136819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62136820	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136822	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136823	0.94[ASN][1000 genomes]
rs62136825	0.94[ASN][1000 genomes]
rs62136827	0.94[ASN][1000 genomes]
rs62140550	0.94[ASN][1000 genomes]
rs62140553	0.88[AMR][1000 genomes]
rs62140556	0.88[AMR][1000 genomes]
rs6544938	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544939	0.92[ASN][1000 genomes]
rs6706031	0.94[ASN][1000 genomes]
rs6715620	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6716381	0.94[ASN][1000 genomes]
rs6722440	0.94[ASN][1000 genomes]
rs6729120	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729604	0.94[ASN][1000 genomes]
rs6733548	0.94[ASN][1000 genomes]
rs6743966	1.00[ASN][1000 genomes]
rs6743994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745578	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6755303	0.92[ASN][1000 genomes]
rs6758093	0.94[ASN][1000 genomes]
rs6758512	0.94[ASN][1000 genomes]
rs71423929	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs720827	0.94[EUR][1000 genomes]
rs7340475	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73926966	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs754411	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7565420	0.89[ASN][1000 genomes]
rs7574514	0.90[ASN][1000 genomes]
rs7574833	0.88[ASN][1000 genomes]
rs7575172	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586004	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7596198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601491	0.94[ASN][1000 genomes]
rs8861	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973504	0.85[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
rs6715391	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47106400-47131000	Weak transcription	Esophagus	oesophagus
2	chr2:47113200-47131200	Weak transcription	Aorta	Aorta
3	chr2:47116000-47133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47116200-47133000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:47116600-47131000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:47116600-47131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:47116600-47131800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:47116600-47132200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:47116600-47132400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:47116600-47132400	Weak transcription	NHEK	skin
11	chr2:47116800-47131000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:47117400-47133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:47117800-47131200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:47120000-47130800	Weak transcription	Left Ventricle	heart
16	chr2:47120000-47133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:47120800-47133000	Weak transcription	Pancreas	Pancrea
18	chr2:47121000-47132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:47121000-47132400	Weak transcription	Hela-S3	cervix
20	chr2:47121000-47132400	Weak transcription	NHDF-Ad	bronchial
21	chr2:47123600-47131000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:47124200-47131000	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:47124400-47131000	Weak transcription	Fetal Intestine Small	intestine
24	chr2:47124800-47132400	Weak transcription	Fetal Lung	lung
25	chr2:47124800-47132800	Weak transcription	NHLF	lung
26	chr2:47125200-47131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:47125200-47132200	Weak transcription	Dnd41	blood
28	chr2:47125400-47132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:47125400-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:47125600-47131200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:47125800-47133200	Weak transcription	Spleen	Spleen
32	chr2:47126000-47131400	Weak transcription	Adipose Nuclei	Adipose
33	chr2:47126000-47132600	Weak transcription	HUVEC	blood vessel
34	chr2:47126000-47133200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:47126000-47137000	Weak transcription	Right Atrium	heart
36	chr2:47126200-47131000	Weak transcription	HepG2	liver
37	chr2:47126400-47131200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:47126400-47132400	Weak transcription	Lung	lung
39	chr2:47126400-47132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:47126600-47131200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:47126600-47131800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:47126800-47131000	Weak transcription	Fetal Intestine Large	intestine
43	chr2:47126800-47131000	Weak transcription	Thymus	Thymus
44	chr2:47126800-47131200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:47126800-47132200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:47127000-47132200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:47127200-47132400	Weak transcription	Brain Angular Gyrus	brain
48	chr2:47127200-47132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:47127200-47133200	Weak transcription	Brain Germinal Matrix	brain
50	chr2:47127400-47131400	Weak transcription	Brain Anterior Caudate	brain

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