Variant report

Variant	rs62140556
Chromosome Location	chr2:47171027-47171028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr2:47170996-47171553	GM12878	blood:	n/a	chr2:47171253-47171262
2	MXI1	chr2:47170417-47171396	GM12878	blood:	n/a	chr2:47170887-47170896
3	PML	chr2:47170238-47171843	GM12878	blood:	n/a	n/a
4	BCLAF1	chr2:47170815-47171789	GM12878	blood:	n/a	chr2:47171253-47171262
5	ATF2	chr2:47171000-47171729	GM12878	blood:	n/a	n/a
6	FOXM1	chr2:47170404-47171603	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:47170932-47171329	GM12891	blood:	n/a	n/a
8	TAF1	chr2:47170959-47171372	GM12878	blood:	n/a	n/a
9	RELA	chr2:47170344-47171702	GM19099	blood:	n/a	n/a
10	POLR2A	chr2:47170331-47171329	GM12891	blood:	n/a	n/a
11	POLR2A	chr2:47170770-47171280	GM12891	blood:	n/a	n/a
12	TAF1	chr2:47170951-47171311	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:47169934-47171448	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:47170434-47171393	GM12892	blood:	n/a	n/a
15	STAT5A	chr2:47170996-47171806	GM12878	blood:	n/a	n/a
16	NFATC1	chr2:47170896-47171620	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:47170199-47171419	GM12892	blood:	n/a	n/a
18	EP300	chr2:47170737-47171427	GM12878	blood:	n/a	n/a
19	ELK1	chr2:47170829-47171374	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:47170194-47171484	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:47168094-47171520	GM12878	blood:	n/a	n/a
22	NFIC	chr2:47170791-47171793	GM12878	blood:	n/a	n/a
23	EP300	chr2:47170918-47171487	GM12878	blood:	n/a	n/a
24	EBF1	chr2:47170970-47171295	GM12878	blood:	n/a	n/a
25	SP1	chr2:47170989-47171498	GM12878	blood:	n/a	n/a
26	WRNIP1	chr2:47170350-47171496	GM12878	blood:	n/a	n/a
27	RUNX3	chr2:47170251-47171811	GM12878	blood:	n/a	n/a
28	RELA	chr2:47170635-47171543	GM18951	blood:	n/a	n/a
29	CHD2	chr2:47170755-47171371	GM12878	blood:	n/a	n/a
30	BCLAF1	chr2:47170998-47171824	GM12878	blood:	n/a	chr2:47171253-47171262
31	RELA	chr2:47170644-47171592	GM12878	blood:	n/a	n/a
32	EBF1	chr2:47170932-47171357	GM12878	blood:	n/a	n/a
33	RELA	chr2:47170558-47171714	GM18505	blood:	n/a	n/a
34	STAT3	chr2:47171027-47171465	GM12878	blood:	n/a	n/a
35	CEBPB	chr2:47170856-47171690	GM12878	blood:	n/a	n/a
36	ATF2	chr2:47170833-47171685	GM12878	blood:	n/a	n/a
37	TBP	chr2:47170793-47171547	GM12878	blood:	n/a	n/a
38	MAZ	chr2:47170990-47171497	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:47170307-47171409	GM12878	blood:	n/a	n/a
40	RELA	chr2:47170580-47171561	GM12892	blood:	n/a	n/a
41	ETS1	chr2:47170951-47171325	GM12878	blood:	n/a	chr2:47171217-47171232 chr2:47171220-47171229 chr2:47171220-47171229 chr2:47171220-47171229 chr2:47171217-47171233 chr2:47171220-47171229
42	ZNF384	chr2:47170996-47171765	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:47168084-47171676	GM12878	blood:	n/a	n/a
44	BATF	chr2:47171013-47171486	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:47168238-47171702	GM12891	blood:	n/a	n/a
46	RCOR1	chr2:47171006-47171732	GM12878	blood:	n/a	n/a
47	MTA3	chr2:47170073-47172114	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:47170654-47171309	GM12892	blood:	n/a	n/a
49	RELA	chr2:47170898-47171450	GM19193	blood:	n/a	n/a
50	POLR2A	chr2:47170547-47171310	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47170300..47176373-chr2:47180929..47185322,6	MCF-7	breast:
2	chr2:47145255..47147590-chr2:47169697..47171236,2	K562	blood:
3	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
4	chr2:47169747..47171383-chr2:47233270..47235359,2	MCF-7	breast:
5	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
6	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17035884	0.82[AMR][1000 genomes]
rs2084192	0.85[AMR][1000 genomes]
rs55872217	0.82[AMR][1000 genomes]
rs56213467	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58589709	0.83[AMR][1000 genomes]
rs60088869	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60194846	0.85[AMR][1000 genomes]
rs62136822	0.82[AMR][1000 genomes]
rs62140553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6715391	0.88[AMR][1000 genomes]
rs6715620	0.85[AMR][1000 genomes]
rs6729120	0.85[AMR][1000 genomes]
rs6743994	0.88[AMR][1000 genomes]
rs6745578	0.84[ASN][1000 genomes]
rs71423929	0.88[AMR][1000 genomes]
rs73926966	0.88[AMR][1000 genomes]
rs7575172	0.85[AMR][1000 genomes]
rs7596198	0.88[AMR][1000 genomes]
rs8861	0.82[AMR][1000 genomes]
rs9973504	0.87[ASN][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47168600-47171400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:47169000-47171200	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr2:47169000-47171400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr2:47169000-47171400	Flanking Active TSS	Brain Hippocampus Middle	brain
5	chr2:47169000-47171600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr2:47169400-47171200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:47169400-47171200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:47169400-47171800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr2:47169400-47178800	Weak transcription	Ovary	ovary
10	chr2:47169400-47179000	Weak transcription	Gastric	stomach
11	chr2:47169600-47171200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr2:47169600-47171200	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr2:47169600-47171200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr2:47169600-47171600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:47169600-47172000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:47169600-47172800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:47169600-47175000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:47169600-47177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:47169600-47177600	Weak transcription	Left Ventricle	heart
20	chr2:47169600-47178800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:47169800-47171200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:47169800-47171200	Transcr. at gene 5' and 3'	Osteobl	bone
24	chr2:47169800-47171400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr2:47169800-47171400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:47169800-47171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:47169800-47171600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:47169800-47171600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr2:47169800-47171800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
30	chr2:47169800-47172800	Weak transcription	Fetal Heart	heart
31	chr2:47169800-47177600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:47169800-47177600	Weak transcription	Fetal Lung	lung
33	chr2:47169800-47178200	Weak transcription	Fetal Brain Female	brain
34	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
36	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
37	chr2:47170000-47171200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr2:47170000-47171200	Enhancers	Small Intestine	intestine
39	chr2:47170000-47171400	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:47170000-47171400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:47170000-47171600	Enhancers	Placenta	Placenta
42	chr2:47170000-47171800	Enhancers	Pancreas	Pancrea
43	chr2:47170000-47171800	Enhancers	Spleen	Spleen
44	chr2:47170000-47177000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:47170000-47177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:47170000-47177600	Weak transcription	Esophagus	oesophagus
47	chr2:47170000-47177800	Weak transcription	Liver	Liver
48	chr2:47170000-47177800	Weak transcription	NH-A	brain
49	chr2:47170000-47178800	Weak transcription	HSMMtube	muscle
50	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel

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