Variant report

Variant	rs72819463
Chromosome Location	chr2:95831094-95831095
allele	A/G
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	CEBPB	chr2:95830935-95831673	GM12878	blood:	n/a	n/a
2	CHD2	chr2:95830962-95832008	GM12878	blood:	n/a	n/a
3	MYC	chr2:95831081-95831591	HUVEC	blood vessel:	n/a	n/a
4	GABPA	chr2:95830862-95831557	K562	blood:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
5	POLR2A	chr2:95830942-95831957	Gliobla	brain:	n/a	n/a
6	POLR2A	chr2:95830747-95831943	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:95830842-95831933	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr2:95830810-95831856	MCF-7	breast:	n/a	n/a
9	TAF1	chr2:95831044-95831711	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr2:95831000-95831712	SK-N-SH	brain:	n/a	n/a
11	FOXM1	chr2:95830889-95831812	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:95830795-95831876	PANC-1	pancreas:	n/a	n/a
13	ZNF143	chr2:95830911-95831983	H1-hESC	embryonic stem cell:	n/a	chr2:95831468-95831486
14	SIN3AK20	chr2:95830916-95831799	SK-N-SH	brain:	n/a	n/a
15	RCOR1	chr2:95831046-95832148	GM12878	blood:	n/a	n/a
16	GABPA	chr2:95830966-95831480	H1-hESC	embryonic stem cell:	n/a	chr2:95831155-95831162 chr2:95831161-95831168
17	POLR2A	chr2:95830780-95831950	GM12878	blood:	n/a	n/a
18	REST	chr2:95830806-95831715	HepG2	liver:	n/a	chr2:95831365-95831383 chr2:95831377-95831384
19	POLR2A	chr2:95830916-95831757	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr2:95830829-95831939	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr2:95830907-95832026	MCF-7	breast:	n/a	n/a
22	GABPA	chr2:95830992-95831509	Hela-S3	cervix:	n/a	chr2:95831155-95831162 chr2:95831161-95831168
23	CEBPB	chr2:95830898-95832157	IMR90	lung:	n/a	chr2:95831970-95831983
24	POLR2A	chr2:95830753-95831867	PANC-1	pancreas:	n/a	n/a
25	MAFK	chr2:95830832-95831654	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr2:95830724-95831979	U87	brain:	n/a	n/a
27	GABPA	chr2:95830792-95831795	HL-60	blood:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
28	PML	chr2:95830913-95831865	MCF-7	breast:	n/a	n/a
29	BCLAF1	chr2:95831003-95831919	GM12878	blood:	n/a	n/a
30	USF1	chr2:95830926-95831662	A549	lung:	n/a	n/a
31	USF1	chr2:95831001-95831524	A549	lung:	n/a	n/a
32	NRF1	chr2:95830978-95831847	GM12878	blood:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831534-95831545 chr2:95831535-95831549 chr2:95831161-95831168
33	NFIC	chr2:95830894-95831759	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:95830751-95831832	PFSK-1	brain:	n/a	n/a
35	TAF1	chr2:95830873-95831933	HepG2	liver:	n/a	n/a
36	GABPA	chr2:95830862-95831616	Hela-S3	cervix:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
37	TAF1	chr2:95831013-95831669	GM12892	blood:	n/a	n/a
38	SP1	chr2:95830907-95831933	A549	lung:	n/a	n/a
39	YY1	chr2:95831077-95831635	NT2-D1	testis:	n/a	chr2:95831385-95831393 chr2:95831382-95831392 chr2:95831380-95831399 chr2:95831382-95831404
40	POLR2A	chr2:95830788-95831868	K562	blood:	n/a	n/a
41	NFIC	chr2:95830762-95831667	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:95830866-95831899	H1-hESC	embryonic stem cell:	n/a	n/a
43	GABPA	chr2:95830511-95832081	MCF-7	breast:	n/a	chr2:95831532-95831546 chr2:95831155-95831162 chr2:95831535-95831544 chr2:95831535-95831546 chr2:95831535-95831549 chr2:95831161-95831168
44	MAX	chr2:95830999-95831770	H1-hESC	embryonic stem cell:	n/a	n/a
45	ATF1	chr2:95831041-95831682	K562	blood:	n/a	n/a
46	CHD2	chr2:95830924-95832030	HepG2	liver:	n/a	n/a
47	FOXA2	chr2:95830925-95831585	A549	lung:	n/a	n/a
48	PML	chr2:95830864-95832022	K562	blood:	n/a	n/a
49	REST	chr2:95830866-95831830	HL-60	blood:	n/a	chr2:95831365-95831383 chr2:95831377-95831384
50	MYC	chr2:95830936-95832156	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:95784064..95788692-chr2:95827645..95832682,10	MCF-7	breast:
2	chr2:95831030..95831865-chr7:5569490..5570227,2	Hela-S3	cervix:
3	chr2:95784303..95789114-chr2:95829766..95832778,9	MCF-7	breast:
4	chr2:95816122..95821729-chr2:95829524..95833130,7	MCF-7	breast:
5	chr11:114271116..114271784-chr2:95830802..95831754,2	Hela-S3	cervix:
6	chr2:95820602..95822831-chr2:95829587..95831468,2	MCF-7	breast:
7	chr2:95830717..95831431-chr7:107220273..107221008,2	HCT-116	colon:
8	chr2:95786108..95790506-chr2:95828555..95834084,9	K562	blood:
9	chr2:95830665..95832278-chr2:95962096..95964714,2	MCF-7	breast:
10	chr2:95830927..95831667-chr2:201753676..201754609,2	NB4	blood:
11	chr2:95829346..95831231-chr2:95961091..95963572,2	MCF-7	breast:
12	chr2:95830116..95832224-chr2:95974723..95976277,2	MCF-7	breast:
13	chr2:95786123..95790193-chr2:95829168..95832965,6	K562	blood:
14	chr2:95829966..95832262-chr2:95871285..95874374,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF514-1	chr2:95829476-95831182	NONHSAT072465

Variant related genes	Relation type
ZNF2	TF binding region
ENSG00000144026	Chromatin interaction
ENSG00000180425	Chromatin interaction
ENSG00000233757	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000076053	Chromatin interaction
ENSG00000255663	Chromatin interaction
ENSG00000075790	Chromatin interaction
ENSG00000115041	Chromatin interaction
ENSG00000240344	Chromatin interaction
ENSG00000272854	Chromatin interaction
ENSG00000144029	Chromatin interaction
ENSG00000196290	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs72819453	0.84[EUR][1000 genomes]
rs72819465	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72819466	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72819479	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72819493	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72819495	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72821406	1.00[AMR][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	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95829800-95832400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:95829800-95832600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:95830000-95831600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr2:95830000-95832000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:95830000-95832000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:95830000-95832000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:95830200-95831400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:95830200-95831800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr2:95830200-95832000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:95830200-95832000	Active TSS	Psoas Muscle	Psoas
11	chr2:95830200-95832000	Active TSS	Stomach Mucosa	stomach
12	chr2:95830200-95832000	Active TSS	HMEC	breast
13	chr2:95830200-95832000	Active TSS	K562	blood
14	chr2:95830200-95832000	Active TSS	NHLF	lung
15	chr2:95830200-95832200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr2:95830200-95832400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:95830200-95832600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:95830400-95831200	Flanking Active TSS	Liver	Liver
19	chr2:95830400-95831600	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr2:95830400-95832000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:95830400-95832000	Active TSS	Brain Substantia Nigra	brain
22	chr2:95830400-95832000	Active TSS	Fetal Heart	heart
23	chr2:95830400-95832000	Active TSS	Fetal Intestine Large	intestine
24	chr2:95830400-95832000	Active TSS	Hela-S3	cervix
25	chr2:95830400-95832200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:95830400-95832200	Active TSS	Right Atrium	heart
27	chr2:95830400-95832200	Active TSS	GM12878-XiMat	blood
28	chr2:95830400-95832400	Active TSS	NHDF-Ad	bronchial
29	chr2:95830400-95832600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:95830400-95832600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr2:95830400-95832600	Active TSS	HSMM	muscle
32	chr2:95830600-95831200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr2:95830600-95831200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:95830600-95831200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:95830600-95831200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr2:95830600-95831200	Flanking Active TSS	Fetal Thymus	thymus
37	chr2:95830600-95831200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:95830600-95831800	Active TSS	Colonic Mucosa	Colon
39	chr2:95830600-95831800	Active TSS	Fetal Muscle Trunk	muscle
40	chr2:95830600-95831800	Active TSS	Placenta	Placenta
41	chr2:95830600-95831800	Active TSS	Ovary	ovary
42	chr2:95830600-95832000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:95830600-95832000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:95830600-95832000	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr2:95830600-95832000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:95830600-95832000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:95830600-95832000	Active TSS	Brain Germinal Matrix	brain
48	chr2:95830600-95832000	Active TSS	HSMMtube	muscle
49	chr2:95830600-95832000	Active TSS	NHEK	skin
50	chr2:95830600-95832200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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