Variant report

Variant	rs2996550
Chromosome Location	chr1:247000748-247000749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr1:246999639-247002277	A549	lung:	n/a	chr1:247001916-247001925
2	POLR2A	chr1:246999486-247002141	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:246999995-247002228	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:247000647-247002456	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:247000286-247002454	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:247000299-247000754	Hela-S3	cervix:	n/a	n/a
7	NFATC1	chr1:247000565-247001432	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:246999482-247002222	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:247000566-247002073	HL-60	blood:	n/a	n/a
10	POLR2A	chr1:247000336-247002239	PFSK-1	brain:	n/a	n/a
11	MTA3	chr1:247000619-247001584	GM12878	blood:	n/a	n/a
12	RUNX3	chr1:247000698-247001391	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:247000361-247002556	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr1:247000739-247001455	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:247000569-247001815	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:247000504-247001901	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr1:247000563-247001552	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:247000185-247003285	K562	blood:	n/a	n/a
19	POLR2A	chr1:246999499-247001898	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr1:247000553-247002562	A549	lung:	n/a	n/a
21	POLR2A	chr1:247000709-247002197	HCT-116	colon:	n/a	n/a
22	PML	chr1:247000693-247001562	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:247000674-247001943	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFATC1	chr1:247000633-247001518	GM12878	blood:	n/a	n/a
25	MTA3	chr1:247000748-247001338	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247000678..247002401-chr1:247004834..247006838,2	K562	blood:
2	chr1:247000376..247002302-chr1:247040440..247042162,2	K562	blood:
3	chr1:246999464..247001183-chr1:247004017..247007456,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252011	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1110068	0.93[GIH][hapmap];0.84[AMR][1000 genomes]
rs1630829	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1691251	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892117	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2800222	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2996549	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5021094	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688227	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526386	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7528980	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530860	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783081	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246989200-247011200	Weak transcription	Fetal Kidney	kidney
2	chr1:246993200-247004200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:246994800-247003200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:246995200-247001400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:246995400-247004200	Weak transcription	HUVEC	blood vessel
6	chr1:246997400-247002200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:246998800-247004200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:246999000-247002400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:246999200-247004600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:246999200-247010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:246999400-247001200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:246999400-247004000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:246999400-247004200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:246999600-247001000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:246999600-247001400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:246999600-247001800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:246999600-247004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:246999600-247004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:246999800-247004400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:246999800-247004400	Weak transcription	Hela-S3	cervix
21	chr1:246999800-247005600	Weak transcription	Ovary	ovary
22	chr1:246999800-247007600	Weak transcription	Right Ventricle	heart
23	chr1:247000000-247002000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:247000000-247002000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:247000200-247001200	Weak transcription	NHEK	skin
26	chr1:247000200-247002000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:247000200-247002000	Weak transcription	HSMM	muscle
28	chr1:247000200-247002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:247000200-247004000	Weak transcription	Osteobl	bone
30	chr1:247000200-247004200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:247000200-247004200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:247000200-247004400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:247000200-247004400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:247000200-247020200	Weak transcription	Spleen	Spleen
35	chr1:247000400-247001600	Enhancers	K562	blood
36	chr1:247000400-247001800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:247000400-247002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:247000600-247002800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:247000600-247003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:247000600-247003200	Weak transcription	Fetal Thymus	thymus
41	chr1:247000600-247003400	Weak transcription	Dnd41	blood
42	chr1:247000600-247004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:247000600-247004600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:247000600-247007800	Weak transcription	Fetal Brain Female	brain

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