Variant report

Variant	rs9973769
Chromosome Location	chr2:47170152-47170153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47170056-47170171	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:47169934-47171448	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:47168094-47171520	GM12878	blood:	n/a	n/a
4	YY1	chr2:47170070-47170398	GM12891	blood:	n/a	n/a
5	YY1	chr2:47170053-47170605	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:47168084-47171676	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:47168238-47171702	GM12891	blood:	n/a	n/a
8	MTA3	chr2:47170073-47172114	GM12878	blood:	n/a	n/a
9	RELA	chr2:47168062-47171777	GM12891	blood:	n/a	n/a
10	POLR2A	chr2:47168586-47171994	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47145255..47147590-chr2:47169697..47171236,2	K562	blood:
2	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
3	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
4	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
5	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
6	chr2:47169747..47171383-chr2:47233270..47235359,2	MCF-7	breast:
7	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
8	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
9	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
10	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

No data

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000180398	Chromatin interaction
ENSG00000272814	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10084332	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10164756	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10165085	0.90[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398748	0.90[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	0.90[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	0.90[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	0.88[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6729569	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755386	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73926967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926970	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926983	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]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9973769	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47167600-47170400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:47167600-47170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:47167600-47170400	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:47167600-47170600	Active TSS	Thymus	Thymus
5	chr2:47167800-47170400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:47168000-47170400	Active TSS	GM12878-XiMat	blood
7	chr2:47168000-47170400	Active TSS	HSMM	muscle
8	chr2:47168000-47170400	Active TSS	NHDF-Ad	bronchial
9	chr2:47168000-47170400	Active TSS	NHLF	lung
10	chr2:47168200-47170200	Active TSS	Colonic Mucosa	Colon
11	chr2:47168600-47170200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:47168600-47171000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:47168600-47171400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:47168800-47170200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr2:47169000-47170200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr2:47169000-47170400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr2:47169000-47170600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:47169000-47170800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:47169000-47171200	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:47169000-47171400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr2:47169000-47171400	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr2:47169000-47171600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:47169200-47170200	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr2:47169200-47170200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr2:47169200-47170600	Flanking Active TSS	Dnd41	blood
26	chr2:47169400-47170200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:47169400-47171200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr2:47169400-47171200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:47169400-47171800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr2:47169400-47178800	Weak transcription	Ovary	ovary
31	chr2:47169400-47179000	Weak transcription	Gastric	stomach
32	chr2:47169600-47170200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:47169600-47170200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr2:47169600-47170200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:47169600-47170200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:47169600-47170200	Active TSS	Brain Substantia Nigra	brain
37	chr2:47169600-47170200	Flanking Active TSS	HMEC	breast
38	chr2:47169600-47170400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:47169600-47170400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr2:47169600-47170400	Weak transcription	Lung	lung
41	chr2:47169600-47170600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr2:47169600-47170600	Flanking Active TSS	HepG2	liver
43	chr2:47169600-47170800	Flanking Active TSS	Hela-S3	cervix
44	chr2:47169600-47171000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:47169600-47171000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:47169600-47171000	Enhancers	Stomach Mucosa	stomach
47	chr2:47169600-47171200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr2:47169600-47171200	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr2:47169600-47171200	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr2:47169600-47171600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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