Variant report

Variant	rs2247539
Chromosome Location	chr7:50133009-50133010
allele	A/C
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	YY1	chr7:50132559-50133038	GM12891	blood:	n/a	n/a
2	MTA3	chr7:50132350-50133234	GM12878	blood:	n/a	n/a
3	MAX	chr7:50132394-50133050	MCF-7	breast:	n/a	n/a
4	RUNX3	chr7:50132176-50133036	GM12878	blood:	n/a	n/a
5	GABPA	chr7:50132674-50133084	GM12878	blood:	n/a	chr7:50132869-50132878
6	GABPA	chr7:50132202-50133194	HL-60	blood:	n/a	chr7:50132869-50132878
7	GABPA	chr7:50132434-50133418	MCF-7	breast:	n/a	chr7:50132869-50132878
8	BCLAF1	chr7:50132671-50133087	GM12878	blood:	n/a	chr7:50132911-50132920 chr7:50132858-50132867
9	YY1	chr7:50132525-50133059	GM12892	blood:	n/a	n/a
10	STAT5A	chr7:50132580-50133040	GM12878	blood:	n/a	n/a
11	GABPA	chr7:50132548-50133144	GM12878	blood:	n/a	chr7:50132869-50132878
12	GABPA	chr7:50132648-50133040	H1-hESC	embryonic stem cell:	n/a	chr7:50132869-50132878
13	POU2F2	chr7:50132692-50133241	GM12891	blood:	n/a	n/a
14	ELF1	chr7:50132483-50133128	GM12878	blood:	n/a	chr7:50132857-50132866
15	YY1	chr7:50132766-50133057	GM12891	blood:	n/a	n/a
16	EGR1	chr7:50132714-50133067	GM12878	blood:	n/a	chr7:50132911-50132920
17	ETS1	chr7:50132691-50133060	GM12878	blood:	n/a	chr7:50132909-50132920 chr7:50132909-50132919 chr7:50132911-50132920 chr7:50132858-50132867 chr7:50132855-50132868 chr7:50132858-50132867 chr7:50132859-50132869 chr7:50132858-50132867 chr7:50132856-50132865 chr7:50132858-50132867
18	POLR2A	chr7:50132537-50133086	MCF-7	breast:	n/a	n/a
19	POLR2A	chr7:50132811-50133015	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr7:50132430-50133087	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr7:50132171-50133089	H1-hESC	embryonic stem cell:	n/a	n/a
22	ELF1	chr7:50132576-50133051	MCF-7	breast:	n/a	chr7:50132857-50132866
23	E2F6	chr7:50132241-50133118	H1-hESC	embryonic stem cell:	n/a	chr7:50132840-50132854 chr7:50132992-50133002
24	POLR2A	chr7:50132653-50133016	GM12878	blood:	n/a	n/a
25	MYC	chr7:50132573-50133107	MCF-7	breast:	n/a	n/a
26	TAF1	chr7:50132681-50133067	GM12878	blood:	n/a	n/a
27	GABPA	chr7:50132440-50133309	MCF-7	breast:	n/a	chr7:50132869-50132878
28	ELF1	chr7:50132502-50133183	GM12878	blood:	n/a	chr7:50132857-50132866
29	SRF	chr7:50132704-50133014	GM12878	blood:	n/a	n/a
30	TEAD4	chr7:50132720-50133016	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr7:50132541-50133093	GM12892	blood:	n/a	n/a
32	RUNX3	chr7:50132388-50133032	GM12878	blood:	n/a	n/a
33	TCF3	chr7:50132706-50133033	GM12878	blood:	n/a	chr7:50132845-50132859 chr7:50132849-50132862
34	GABPA	chr7:50132567-50133224	HL-60	blood:	n/a	chr7:50132869-50132878
35	BCLAF1	chr7:50132613-50133116	GM12878	blood:	n/a	chr7:50132911-50132920 chr7:50132858-50132867
36	POLR2A	chr7:50132613-50133059	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:50132977-50133027	HCM	heart:	n/a
2	chr7:50132975-50133025	HepG2	liver:	n/a
3	chr7:50133000-50133050	CMK	blood:	n/a
4	chr7:50132977-50133027	HepG2	liver:	n/a
5	chr7:50133000-50133050	HCM	heart:	n/a
6	chr7:50132975-50133025	HCPEpiC	choroid plexus:	n/a
7	chr7:50132975-50133025	SK-N-SH	brain:	n/a
8	chr7:50133000-50133050	ECC-1	luminal epithelium:	n/a
9	chr7:50132975-50133025	GM12878	blood:	n/a
10	chr7:50132975-50133025	HRE	kidney:	n/a
11	chr7:50132975-50133025	MCF-7	breast:	n/a
12	chr7:50133000-50133050	NH-A	brain:	n/a
13	chr7:50133000-50133050	HCF	heart:	n/a
14	chr7:50133000-50133050	PANC-1	pancreas:	n/a
15	chr7:50132975-50133025	SAEC	small airway:	n/a
16	chr7:50132975-50133025	HMEC	breast:	n/a
17	chr7:50132977-50133027	AG04449	skin:	fetal
18	chr7:50133000-50133050	GM12892	blood:	n/a
19	chr7:50132977-50133027	HIPEpiC	eye:	n/a
20	chr7:50132975-50133025	NHDF-neo	bronchial:	n/a
21	chr7:50132975-50133025	Caco-2	colon:	n/a
22	chr7:50133000-50133050	GM12891	blood:	n/a
23	chr7:50132977-50133027	HRPEpiC	eye:	n/a
24	chr7:50133000-50133050	HPAEpiC	pulmonary alveolar:	n/a
25	chr7:50132975-50133025	GM06990	blood:	n/a
26	chr7:50132977-50133027	GM06990	blood:	n/a
27	chr7:50132977-50133027	CMK	blood:	n/a
28	chr7:50132977-50133027	GM12892	blood:	n/a
29	chr7:50132975-50133025	BE2_C	brain:	n/a
30	chr7:50133000-50133050	SK-N-MC	brain:	n/a
31	chr7:50133000-50133050	U87	brain:	n/a
32	chr7:50133000-50133050	LNCaP	prostate:	n/a
33	chr7:50132977-50133027	RPTEC	kidney:	n/a
34	chr7:50132977-50133027	IMR90	lung:	fetal
35	chr7:50133000-50133050	BE2_C	brain:	n/a
36	chr7:50133000-50133050	HRE	kidney:	n/a
37	chr7:50133000-50133050	SK-N-SH	brain:	n/a
38	chr7:50132977-50133027	HEEpiC	esophagus:	n/a
39	chr7:50133000-50133050	AG04449	skin:	fetal
40	chr7:50132977-50133027	U87	brain:	n/a
41	chr7:50132975-50133025	HCF	heart:	n/a
42	chr7:50133000-50133050	MCF10A-Er-Src	breast:	n/a
43	chr7:50133000-50133050	HEK293	kidney:	embryo
44	chr7:50132975-50133025	NH-A	brain:	n/a
45	chr7:50132977-50133027	BE2_C	brain:	n/a
46	chr7:50132977-50133027	Hela-S3	cervix:	n/a
47	chr7:50132977-50133027	MCF10A-Er-Src	breast:	n/a
48	chr7:50132975-50133025	PrEC	prostate:	n/a
49	chr7:50132975-50133025	HEK293	kidney:	embryo
50	chr7:50132975-50133025	HPAEpiC	pulmonary alveolar:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf72-1	chr7:50132920-50133326	NONHSAT120545

Variant related genes	Relation type
ZPBP	TF binding region
C7orf72	TF binding region
ZPBP	CpG island
C7orf72	CpG island

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1351692	0.85[ASN][1000 genomes]
rs1379174	0.85[AMR][1000 genomes]
rs1379175	0.85[AMR][1000 genomes]
rs1508412	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911748	0.93[ASN][1000 genomes]
rs1911749	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1911750	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911757	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1911758	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2174929	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2202772	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2221657	0.86[AMR][1000 genomes]
rs2247628	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366027	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2366028	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2366029	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2886552	0.85[ASN][1000 genomes]
rs3807323	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3807324	0.86[AMR][1000 genomes]
rs3823541	0.86[AMR][1000 genomes]
rs4019793	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4917107	0.83[ASN][1000 genomes]
rs4917109	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4917110	0.93[ASN][1000 genomes]
rs4917111	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4917112	0.86[AMR][1000 genomes]
rs6583423	0.86[AMR][1000 genomes]
rs6583426	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6944215	0.85[ASN][1000 genomes]
rs6956098	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464444	chr7:49671882-50454736	Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv606897	chr7:49671883-50454736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv498090	chr7:49708644-50427714	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1020869	chr7:49712860-50457544	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv830997	chr7:49970866-50136498	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv830998	chr7:50103183-50156564	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50132200-50133200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:50132200-50133200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr7:50132200-50133200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr7:50132200-50133200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:50132200-50133200	Active TSS	Brain Hippocampus Middle	brain
6	chr7:50132200-50133200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr7:50132200-50133200	Active TSS	Fetal Brain Female	brain
8	chr7:50132200-50133200	Active TSS	Fetal Intestine Small	intestine
9	chr7:50132200-50133200	Active TSS	Fetal Kidney	kidney
10	chr7:50132200-50133200	Active TSS	GM12878-XiMat	blood
11	chr7:50132400-50133200	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr7:50132800-50133200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr7:50132800-50133200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:50132800-50133200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr7:50132800-50133200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:50132800-50133200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:50132800-50133200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:50132800-50133200	Active TSS	Liver	Liver
19	chr7:50132800-50133200	Active TSS	Duodenum Mucosa	Duodenum
20	chr7:50132800-50133200	Flanking Active TSS	Fetal Thymus	thymus
21	chr7:50132800-50133200	Flanking Active TSS	Pancreas	Pancrea
22	chr7:50132800-50133200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr7:50133000-50133200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr7:50133000-50133200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:50133000-50133200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr7:50133000-50133200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr7:50133000-50133200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr7:50133000-50133200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:50133000-50133200	Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr7:50133000-50133200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:50133000-50133200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:50133000-50133200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr7:50133000-50133200	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr7:50133000-50133200	Bivalent Enhancer	Left Ventricle	heart
35	chr7:50133000-50133600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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