Variant report

Variant	rs6747288
Chromosome Location	chr2:46772646-46772647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr2:46772427-46772666	GM12878	blood:	n/a	n/a
2	POU2F2	chr2:46772417-46772929	GM12878	blood:	n/a	n/a
3	RCOR1	chr2:46772403-46772847	GM12878	blood:	n/a	n/a
4	FOXM1	chr2:46772197-46772873	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr2:46772290-46772795	GM12878	blood:	n/a	n/a
6	EP300	chr2:46772432-46772652	GM12878	blood:	n/a	chr2:46772501-46772515
7	EP300	chr2:46772408-46772783	GM12878	blood:	n/a	chr2:46772501-46772515
8	TBP	chr2:46772437-46772758	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:46768678-46773017	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:46770477-46777171	GM12878	blood:	n/a	n/a
11	BHLHE40	chr2:46772401-46772802	GM12878	blood:	n/a	n/a
12	RFX5	chr2:46770190-46772854	SK-N-SH	brain:	n/a	chr2:46770339-46770347
13	SIN3A	chr2:46772459-46772655	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr2:46772416-46772678	K562	blood:	n/a	n/a
15	CCNT2	chr2:46772148-46772769	K562	blood:	n/a	n/a
16	POU2F2	chr2:46772542-46772745	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:46770217-46773424	GM12878	blood:	n/a	n/a
18	JUND	chr2:46772418-46772658	K562	blood:	n/a	n/a
19	ZNF143	chr2:46772598-46772909	GM12878	blood:	n/a	n/a
20	ATF2	chr2:46772265-46772849	GM12878	blood:	n/a	n/a
21	EP300	chr2:46772392-46772685	K562	blood:	n/a	chr2:46772501-46772515
22	BCLAF1	chr2:46772334-46772894	GM12878	blood:	n/a	n/a
23	RUNX3	chr2:46772095-46772992	GM12878	blood:	n/a	n/a
24	RCOR1	chr2:46772516-46772817	K562	blood:	n/a	n/a
25	ATF2	chr2:46772300-46772848	GM12878	blood:	n/a	n/a
26	MXI1	chr2:46772199-46772874	GM12878	blood:	n/a	n/a
27	IKZF1	chr2:46772480-46772666	GM12878	blood:	n/a	n/a
28	CEBPD	chr2:46772282-46772716	K562	blood:	n/a	n/a
29	RUNX3	chr2:46772103-46772951	GM12878	blood:	n/a	n/a
30	CUX1	chr2:46772108-46772664	K562	blood:	n/a	n/a
31	PML	chr2:46772427-46772647	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:46768760-46773354	GM18505	blood:	n/a	n/a
33	POLR2A	chr2:46772510-46773055	GM12878	blood:	n/a	n/a
34	MTA3	chr2:46771378-46773074	GM12878	blood:	n/a	n/a
35	RCOR1	chr2:46772043-46772913	K562	blood:	n/a	n/a
36	ATF1	chr2:46772353-46772678	K562	blood:	n/a	n/a
37	MXI1	chr2:46766247-46772861	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr2:46771967-46772852	GM12878	blood:	n/a	n/a
39	TEAD4	chr2:46772258-46772780	K562	blood:	n/a	n/a
40	NFATC1	chr2:46772347-46772915	GM12878	blood:	n/a	n/a
41	STAT3	chr2:46772419-46772720	GM12878	blood:	n/a	n/a
42	CUX1	chr2:46772223-46772842	GM12878	blood:	n/a	n/a
43	NFYB	chr2:46772053-46772673	GM12878	blood:	n/a	chr2:46772300-46772314 chr2:46772299-46772314 chr2:46772299-46772314
44	WRNIP1	chr2:46772638-46772831	GM12878	blood:	n/a	n/a
45	NFIC	chr2:46772266-46772867	GM12878	blood:	n/a	n/a
46	STAT3	chr2:46772613-46772655	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr2:46770819-46773352	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46770485..46772962-chr2:46842113..46844264,3	MCF-7	breast:
2	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
3	chr2:46770414..46772957-chr2:46801807..46804486,2	MCF-7	breast:
4	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:
5	chr2:46767796..46769414-chr2:46769669..46772927,3	MCF-7	breast:
6	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:

No data

Variant related genes	Relation type
ATP6V1E2	TF binding region
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000253515	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1376405	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1993077	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2053900	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754552	0.96[ASN][1000 genomes]
rs4952832	0.88[ASN][1000 genomes]
rs6714484	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7565377	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7568909	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46770200-46773000	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr2:46770600-46772800	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr2:46770600-46773000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr2:46771000-46772800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:46771000-46774000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:46771000-46776600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:46771200-46772800	Flanking Active TSS	GM12878-XiMat	blood
9	chr2:46771200-46772800	Enhancers	K562	blood
10	chr2:46771200-46774200	Weak transcription	Liver	Liver
11	chr2:46771200-46774200	Weak transcription	Esophagus	oesophagus
12	chr2:46771200-46774400	Weak transcription	Ovary	ovary
13	chr2:46771200-46774400	Weak transcription	Thymus	Thymus
14	chr2:46771200-46774600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:46771200-46774800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:46771200-46778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
18	chr2:46771200-46781400	Weak transcription	NHEK	skin
19	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:46771400-46773200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:46771400-46774000	Weak transcription	Small Intestine	intestine
24	chr2:46771400-46774400	Weak transcription	Pancreas	Pancrea
25	chr2:46771400-46774800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:46771400-46777000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:46771400-46778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
29	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
32	chr2:46771600-46772800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:46771600-46773000	Enhancers	Spleen	Spleen
34	chr2:46771600-46773200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr2:46771600-46773400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:46771600-46773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:46771600-46773800	Weak transcription	HepG2	liver
38	chr2:46771600-46774000	Weak transcription	Primary T cells from cord blood	blood
39	chr2:46771600-46774200	Weak transcription	Fetal Intestine Large	intestine
40	chr2:46771600-46774600	Weak transcription	Fetal Brain Female	brain
41	chr2:46771600-46777000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:46771600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:46771600-46781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:46771800-46772800	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:46771800-46773000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:46771800-46773000	Enhancers	Colonic Mucosa	Colon
47	chr2:46771800-46773000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:46771800-46773000	Enhancers	Fetal Thymus	thymus
49	chr2:46771800-46773400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:46771800-46773600	Enhancers	Brain Hippocampus Middle	brain

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