Variant report

Variant	rs12534598
Chromosome Location	chr7:107220096-107220097
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:107219987-107221179	PANC-1	pancreas:	n/a	n/a
2	YY1	chr7:107220039-107221269	SK-N-SH_RA	brain:	n/a	chr7:107220669-107220680 chr7:107220398-107220407 chr7:107220659-107220670
3	CEBPB	chr7:107219973-107220744	MCF-7	breast:	n/a	n/a
4	ZKSCAN1	chr7:107220061-107220950	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr7:107220060-107220210	HCPEpiC	choroid plexus:	n/a	n/a
6	POLR2A	chr7:107219976-107221286	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr7:107219908-107221335	H1-hESC	embryonic stem cell:	n/a	n/a
8	HDAC2	chr7:107220063-107221177	MCF-7	breast:	n/a	n/a
9	CEBPB	chr7:107220055-107220575	A549	lung:	n/a	n/a
10	CREB1	chr7:107220059-107220979	H1-hESC	embryonic stem cell:	n/a	n/a
11	HCFC1	chr7:107220070-107221262	K562	blood:	n/a	n/a
12	BRCA1	chr7:107220080-107221406	Hela-S3	cervix:	n/a	n/a
13	REST	chr7:107220007-107220733	A549	lung:	n/a	chr7:107220667-107220680
14	MAX	chr7:107220024-107221458	A549	lung:	n/a	chr7:107220666-107220676
15	RAD21	chr7:107220075-107221242	IMR90	lung:	n/a	n/a
16	POLR2A	chr7:107220002-107220905	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr7:107220076-107221245	MCF-7	breast:	n/a	n/a
18	TAF1	chr7:107220096-107221204	K562	blood:	n/a	n/a
19	TEAD4	chr7:107219933-107221333	K562	blood:	n/a	n/a
20	POLR2A	chr7:107220091-107221312	HL-60	blood:	n/a	n/a
21	SIN3AK20	chr7:107219990-107221247	SK-N-SH	brain:	n/a	n/a
22	CREB1	chr7:107220090-107221203	HepG2	liver:	n/a	n/a
23	CTCF	chr7:107220020-107222615	SK-N-SH	brain:	n/a	chr7:107220614-107220627
24	POLR2A	chr7:107219993-107221362	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr7:107220096-107221234	K562	blood:	n/a	n/a
26	IRF1	chr7:107220078-107221157	K562	blood:	n/a	n/a
27	HEY1	chr7:107220044-107221200	K562	blood:	n/a	chr7:107220790-107220805
28	SIN3AK20	chr7:107220041-107221381	K562	blood:	n/a	n/a
29	BCL3	chr7:107219957-107220571	A549	lung:	n/a	chr7:107220398-107220411
30	POLR2A	chr7:107219716-107222424	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr7:107220072-107221184	HCT-116	colon:	n/a	n/a
32	REST	chr7:107220089-107221204	SK-N-SH	brain:	n/a	chr7:107220667-107220680 chr7:107221061-107221074
33	TRIM28	chr7:107219976-107221328	K562	blood:	n/a	n/a
34	RCOR1	chr7:107220088-107221207	K562	blood:	n/a	n/a
35	MAX	chr7:107220026-107221294	MCF-7	breast:	n/a	chr7:107220666-107220676
36	HEY1	chr7:107219978-107221274	K562	blood:	n/a	chr7:107220790-107220805
37	MAX	chr7:107220021-107221264	K562	blood:	n/a	chr7:107220666-107220676
38	CEBPD	chr7:107220048-107221310	K562	blood:	n/a	n/a
39	MAX	chr7:107220092-107221309	HepG2	liver:	n/a	chr7:107220666-107220676
40	BRCA1	chr7:107220078-107220219	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr7:107220070-107221271	HepG2	liver:	n/a	n/a
42	PML	chr7:107219974-107221309	K562	blood:	n/a	n/a
43	POLR2A	chr7:107219973-107221268	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr7:107220041-107221233	Hela-S3	cervix:	n/a	n/a
45	MAX	chr7:107220068-107221267	NB4	blood:	n/a	chr7:107220666-107220676
46	MXI1	chr7:107219592-107222186	SK-N-SH	brain:	n/a	n/a
47	CREB1	chr7:107220095-107221246	K562	blood:	n/a	n/a
48	POLR2A	chr7:107220050-107221324	K562	blood:	n/a	n/a
49	NR2F2	chr7:107219893-107221914	K562	blood:	n/a	n/a
50	UBTF	chr7:107220055-107221317	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:107220080-107220130	SKMC	muscle:	n/a
2	chr7:107220080-107220130	HCPEpiC	choroid plexus:	n/a
3	chr7:107220080-107220130	MCF-7	breast:	n/a
4	chr7:107220080-107220130	GM12878	blood:	n/a
5	chr7:107220080-107220130	NHDF-neo	bronchial:	n/a
6	chr7:107220080-107220130	NH-A	brain:	n/a
7	chr7:107220080-107220130	BE2_C	brain:	n/a
8	chr7:107220080-107220130	HEEpiC	esophagus:	n/a
9	chr7:107220080-107220130	SK-N-SH	brain:	n/a
10	chr7:107220080-107220130	GM06990	blood:	n/a
11	chr7:107220080-107220130	AG04449	skin:	fetal
12	chr7:107220080-107220130	H1-hESC	embryonic stem cell:	embryo
13	chr7:107220080-107220130	HL-60	blood:	n/a
14	chr7:107220080-107220130	IMR90	lung:	fetal
15	chr7:107220080-107220130	HMEC	breast:	n/a
16	chr7:107220080-107220130	K562	blood:	n/a
17	chr7:107220080-107220130	RPTEC	kidney:	n/a
18	chr7:107220080-107220130	SAEC	small airway:	n/a
19	chr7:107220080-107220130	AG09319	gingival:	n/a
20	chr7:107220080-107220130	HCM	heart:	n/a
21	chr7:107220080-107220130	NT2-D1	testis:	n/a
22	chr7:107220080-107220130	LNCaP	prostate:	n/a
23	chr7:107220080-107220130	AG09309	skin:	n/a
24	chr7:107220080-107220130	Hela-S3	cervix:	n/a
25	chr7:107220080-107220130	Jurkat	blood:	n/a
26	chr7:107220080-107220130	AG04450	lung:	fetal
27	chr7:107220080-107220130	HCT-116	colon:	n/a
28	chr7:107220080-107220130	AG10803	skin:	n/a
29	chr7:107220080-107220130	PFSK-1	brain:	n/a
30	chr7:107220080-107220130	GM19239	blood:	n/a
31	chr7:107220080-107220130	ovcar-3	ovarian:	n/a
32	chr7:107220080-107220130	U87	brain:	n/a
33	chr7:107220080-107220130	HIPEpiC	eye:	n/a
34	chr7:107220080-107220130	HPAEpiC	pulmonary alveolar:	n/a
35	chr7:107220080-107220130	GM12892	blood:	n/a
36	chr7:107220080-107220130	Hepatocyte	liver:	n/a
37	chr7:107220080-107220130	CMK	blood:	n/a
38	chr7:107220080-107220130	ProgFib	skin:	n/a
39	chr7:107220080-107220130	PANC-1	pancreas:	n/a
40	chr7:107220080-107220130	HAEpiC	amniotic membrane:	n/a
41	chr7:107220080-107220130	MCF10A-Er-Src	breast:	n/a
42	chr7:107220080-107220130	HRE	kidney:	n/a
43	chr7:107220080-107220130	BJ	skin:	n/a
44	chr7:107220080-107220130	HUVEC	blood vessel:	n/a
45	chr7:107220080-107220130	HRPEpiC	eye:	n/a
46	chr7:107220080-107220130	A549	lung:	n/a
47	chr7:107220080-107220130	HNPCEpiC	eye:	n/a
48	chr7:107220080-107220130	HEK293	kidney:	embryo
49	chr7:107220080-107220130	ECC-1	luminal epithelium:	n/a
50	chr7:107220080-107220130	SK-N-SH_RA	brain:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107188089..107190681-chr7:107220054..107222160,2	MCF-7	breast:
2	chr7:107213853..107217373-chr7:107218524..107221215,3	MCF-7	breast:
3	chr7:107219336..107222149-chr7:107234347..107238081,3	MCF-7	breast:
4	chr7:107219444..107222929-chr7:107242777..107244829,3	MCF-7	breast:
5	chr1:92763878..92764562-chr7:107220034..107220754,2	Hela-S3	cervix:
6	chr7:107217896..107220327-chr7:107230749..107233024,2	MCF-7	breast:
7	chr7:107202748..107209925-chr7:107217558..107222659,11	MCF-7	breast:
8	chr7:107202021..107207492-chr7:107217594..107222531,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COG5-4	chr7:107220002-107220502	ENSG00000272854.1

No data

Variant related genes	Relation type
BCAP29	TF binding region
BCAP29	CpG island
ENSG00000122484	Chromatin interaction
ENSG00000164597	Chromatin interaction
ENSG00000105865	Chromatin interaction
ENSG00000174842	Chromatin interaction
ENSG00000075790	Chromatin interaction
ENSG00000238832	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1024401	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10267978	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11761775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12668615	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12674273	0.85[AMR][1000 genomes]
rs1468335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2520258	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2520262	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2520270	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2520276	0.82[ASN][1000 genomes]
rs2701678	0.82[JPT][hapmap]
rs2701679	0.82[JPT][hapmap]
rs2712203	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2712227	0.81[CEU][hapmap]
rs35868979	0.84[AMR][1000 genomes]
rs3779496	0.88[AFR][1000 genomes]
rs3823958	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4357220	0.83[AMR][1000 genomes]
rs4727682	0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes]
rs4730244	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6466174	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6945488	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs711442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv608074	chr7:107179131-107260856	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv888940	chr7:107210383-107229618	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12534598	FABP2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107205000-107220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:107205000-107220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:107211200-107220200	Weak transcription	Spleen	Spleen
4	chr7:107219600-107220200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr7:107219600-107220400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr7:107219600-107220400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:107219600-107220400	Active TSS	Right Atrium	heart
8	chr7:107219600-107221400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:107219600-107221600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:107219600-107221600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:107219600-107221600	Active TSS	Hela-S3	cervix
12	chr7:107219600-107221600	Active TSS	HUVEC	blood vessel
13	chr7:107219600-107221600	Active TSS	K562	blood
14	chr7:107219600-107221800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:107219600-107222000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:107219600-107222200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:107219600-107222600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:107219600-107223200	Active TSS	Aorta	Aorta
19	chr7:107219800-107220200	Flanking Active TSS	Dnd41	blood
20	chr7:107219800-107220200	Flanking Active TSS	Osteobl	bone
21	chr7:107219800-107220400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr7:107219800-107220400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:107219800-107220400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr7:107219800-107221000	Active TSS	Primary hematopoietic stem cells	blood
25	chr7:107219800-107221200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:107219800-107221400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr7:107219800-107221400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr7:107219800-107221400	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr7:107219800-107221400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:107219800-107221400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:107219800-107221400	Active TSS	Fetal Lung	lung
32	chr7:107219800-107221600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:107219800-107221600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr7:107219800-107221600	Active TSS	A549	lung
35	chr7:107219800-107221600	Active TSS	GM12878-XiMat	blood
36	chr7:107219800-107221600	Active TSS	NH-A	brain
37	chr7:107219800-107221800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr7:107219800-107221800	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr7:107219800-107221800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr7:107219800-107221800	Active TSS	Fetal Muscle Leg	muscle
41	chr7:107219800-107222200	Active TSS	HMEC	breast
42	chr7:107219800-107222200	Active TSS	NHEK	skin
43	chr7:107219800-107222200	Active TSS	NHLF	lung
44	chr7:107219800-107222600	Active TSS	Brain Hippocampus Middle	brain
45	chr7:107219800-107222600	Active TSS	Left Ventricle	heart
46	chr7:107219800-107223000	Active TSS	NHDF-Ad	bronchial
47	chr7:107219800-107223600	Active TSS	Right Ventricle	heart
48	chr7:107220000-107220200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:107220000-107220200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr7:107220000-107220200	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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