Variant report

Variant	rs62190900
Chromosome Location	chr2:208890915-208890916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:208889996-208890934	HepG2	liver:	n/a	n/a
2	MBD4	chr2:208889850-208891008	HepG2	liver:	n/a	n/a
3	MYBL2	chr2:208889618-208891037	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:208890728-208890986	HepG2	liver:	n/a	n/a
5	MXI1	chr2:208888887-208891061	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:208889927-208890997	HL-60	blood:	n/a	n/a
7	MAZ	chr2:208889673-208890941	IMR90	lung:	n/a	n/a
8	POLR2A	chr2:208889944-208890932	GM19193	blood:	n/a	n/a
9	SIN3A	chr2:208890906-208890972	H1-hESC	embryonic stem cell:	n/a	n/a
10	RUNX3	chr2:208890035-208891011	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:208889903-208890929	GM12891	blood:	n/a	n/a
12	POLR2A	chr2:208889822-208890967	GM12892	blood:	n/a	n/a
13	TBL1XR1	chr2:208890771-208890918	K562	blood:	n/a	n/a
14	RUNX3	chr2:208889994-208891025	GM12878	blood:	n/a	n/a
15	MTA3	chr2:208889787-208891003	GM12878	blood:	n/a	n/a
16	FOXP2	chr2:208890650-208890943	SK-N-MC	brain:	n/a	n/a
17	RCOR1	chr2:208890103-208891067	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:208889891-208891050	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr2:208889976-208890931	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:208889921-208890973	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:208889757-208890951	GM12891	blood:	n/a	n/a
22	RCOR1	chr2:208890760-208890955	HepG2	liver:	n/a	n/a
23	REST	chr2:208889929-208890959	HL-60	blood:	n/a	chr2:208890216-208890226 chr2:208890292-208890305
24	POLR2A	chr2:208890019-208890966	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr2:208889951-208890941	GM12891	blood:	n/a	n/a
26	REST	chr2:208889460-208891050	H1-neurons	neurons:	n/a	chr2:208890216-208890226 chr2:208890292-208890305
27	POLR2A	chr2:208890025-208890934	GM12891	blood:	n/a	n/a
28	MAX	chr2:208889818-208891011	HepG2	liver:	n/a	n/a
29	MXI1	chr2:208889523-208891029	IMR90	lung:	n/a	n/a
30	MTA3	chr2:208890092-208890928	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:208889966-208890916	GM18505	blood:	n/a	n/a
32	ZNF143	chr2:208890844-208891044	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:208889862-208891010	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:208889948-208890983	HL-60	blood:	n/a	n/a
35	CHD1	chr2:208889754-208891136	IMR90	lung:	n/a	n/a
36	GABPA	chr2:208889758-208890923	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:208883906..208887647-chr2:208888508..208891752,4	MCF-7	breast:
2	chr2:208883791..208887954-chr2:208888473..208891537,5	MCF-7	breast:
3	chr2:208633363..208636354-chr2:208889689..208891369,2	MCF-7	breast:

No data

Variant related genes	Relation type
PLEKHM3	TF binding region
ENSG00000163251	Chromatin interaction
ENSG00000212246	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10932224	0.82[EUR][1000 genomes]
rs12465292	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12471242	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13431014	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1452521	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17459574	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17459758	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17537670	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17538061	0.81[EUR][1000 genomes]
rs2362787	0.83[EUR][1000 genomes]
rs28463196	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4502388	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190863	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190896	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62190898	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190904	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190905	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192772	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62192773	0.89[EUR][1000 genomes]
rs6435402	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6740362	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72969822	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72981543	0.85[EUR][1000 genomes]
rs7565251	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7588162	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs930745	0.94[AMR][1000 genomes];0.87[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208889400-208891000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:208889400-208891000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:208889400-208891000	Active TSS	Colon Smooth Muscle	Colon
4	chr2:208889400-208891000	Active TSS	Thymus	Thymus
5	chr2:208889600-208891000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:208889600-208891000	Active TSS	Brain Hippocampus Middle	brain
7	chr2:208889600-208891000	Active TSS	Ovary	ovary
8	chr2:208889800-208891000	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:208889800-208891000	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr2:208889800-208891000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:208889800-208891000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:208890200-208891200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr2:208890400-208891000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:208890400-208891000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:208890400-208891000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr2:208890400-208891000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:208890400-208891000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:208890400-208891000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:208890400-208891000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:208890400-208891000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr2:208890400-208891000	Flanking Active TSS	Colonic Mucosa	Colon
22	chr2:208890400-208891000	Flanking Active TSS	Fetal Brain Male	brain
23	chr2:208890400-208891000	Flanking Active TSS	Fetal Lung	lung
24	chr2:208890400-208891000	Flanking Active TSS	Fetal Stomach	stomach
25	chr2:208890400-208891000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:208890400-208891000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr2:208890400-208891000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:208890400-208891000	Flanking Active TSS	A549	lung
29	chr2:208890400-208891000	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:208890400-208891000	Flanking Active TSS	HepG2	liver
31	chr2:208890400-208891000	Flanking Active TSS	NH-A	brain
32	chr2:208890400-208891000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr2:208890400-208891000	Flanking Active TSS	NHEK	skin
34	chr2:208890400-208891200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr2:208890400-208891200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:208890600-208891000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:208890600-208891000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:208890600-208891000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:208890600-208891000	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:208890600-208891000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr2:208890600-208891000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:208890600-208891000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:208890600-208891000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr2:208890600-208891000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:208890600-208891000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:208890600-208891000	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr2:208890600-208891000	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr2:208890600-208891000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:208890600-208891000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:208890600-208891000	Flanking Active TSS	Brain Substantia Nigra	brain

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