Variant report

Variant	rs10799340
Chromosome Location	chr1:226375267-226375268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226373447-226375324	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:226375238-226375290	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:226374223-226375272	K562	blood:	n/a	n/a
4	POLR2A	chr1:226373047-226375319	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:226375201-226375342	MCF-7	breast:	n/a	n/a
6	MXI1	chr1:226372734-226375432	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:226375224-226375274	RPTEC	kidney:	n/a
2	chr1:226375224-226375274	H1-hESC	embryonic stem cell:	embryo
3	chr1:226375224-226375274	IMR90	lung:	fetal
4	chr1:226375224-226375274	MCF-7	breast:	n/a
5	chr1:226375224-226375274	GM06990	blood:	n/a
6	chr1:226375224-226375274	Caco-2	colon:	n/a
7	chr1:226375224-226375274	AG09309	skin:	n/a
8	chr1:226375224-226375274	SK-N-SH_RA	brain:	n/a
9	chr1:226375224-226375274	HEK293	kidney:	embryo
10	chr1:226375224-226375274	A549	lung:	n/a
11	chr1:226375224-226375274	ProgFib	skin:	n/a
12	chr1:226375224-226375274	HRE	kidney:	n/a
13	chr1:226375224-226375274	CMK	blood:	n/a
14	chr1:226375224-226375274	BJ	skin:	n/a
15	chr1:226375224-226375274	ovcar-3	ovarian:	n/a
16	chr1:226375224-226375274	HEEpiC	esophagus:	n/a
17	chr1:226375224-226375274	SK-N-MC	brain:	n/a
18	chr1:226375224-226375274	NHDF-neo	bronchial:	n/a
19	chr1:226375224-226375274	ECC-1	luminal epithelium:	n/a
20	chr1:226375224-226375274	NHBE	bronchial:	n/a
21	chr1:226375224-226375274	AG09319	gingival:	n/a
22	chr1:226375224-226375274	HL-60	blood:	n/a
23	chr1:226375224-226375274	SK-N-SH	brain:	n/a
24	chr1:226375224-226375274	AoSMC	blood vessel:	n/a
25	chr1:226375224-226375274	HCPEpiC	choroid plexus:	n/a
26	chr1:226375224-226375274	NB4	blood:	n/a
27	chr1:226375224-226375274	K562	blood:	n/a
28	chr1:226375224-226375274	Hela-S3	cervix:	n/a
29	chr1:226375224-226375274	HRPEpiC	eye:	n/a
30	chr1:226375224-226375274	GM12892	blood:	n/a
31	chr1:226375224-226375274	Jurkat	blood:	n/a
32	chr1:226375224-226375274	HRCEpiC	kidney:	n/a
33	chr1:226375224-226375274	HAEpiC	amniotic membrane:	n/a
34	chr1:226375224-226375274	LNCaP	prostate:	n/a
35	chr1:226375224-226375274	HPAEpiC	pulmonary alveolar:	n/a
36	chr1:226375224-226375274	AG04449	skin:	fetal
37	chr1:226375224-226375274	AG04450	lung:	fetal
38	chr1:226375224-226375274	NT2-D1	testis:	n/a
39	chr1:226375224-226375274	HMEC	breast:	n/a
40	chr1:226375224-226375274	HNPCEpiC	eye:	n/a
41	chr1:226375224-226375274	SAEC	small airway:	n/a
42	chr1:226375224-226375274	HCM	heart:	n/a
43	chr1:226375224-226375274	HIPEpiC	eye:	n/a
44	chr1:226375224-226375274	BE2_C	brain:	n/a
45	chr1:226375224-226375274	HepG2	liver:	n/a
46	chr1:226375224-226375274	GM12878	blood:	n/a
47	chr1:226375224-226375274	PrEC	prostate:	n/a
48	chr1:226375224-226375274	GM12891	blood:	n/a
49	chr1:226375224-226375274	HUVEC	blood vessel:	n/a
50	chr1:226375224-226375274	SKMC	muscle:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226372831..226375478-chr1:226375885..226377759,2	MCF-7	breast:
2	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
3	chr1:226251379..226253297-chr1:226374542..226377353,2	K562	blood:
4	chr1:226374796..226376428-chr1:226594450..226597292,2	K562	blood:
5	chr1:226374445..226376011-chr1:226411656..226414406,2	K562	blood:
6	chr1:226270770..226272699-chr1:226374583..226377096,2	MCF-7	breast:
7	chr1:226313633..226315169-chr1:226374399..226376035,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACBD3	TF binding region
ACBD3	CpG island
ENSG00000225518	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000185155	Chromatin interaction
ENSG00000223570	Chromatin interaction
ENSG00000143799	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10732276	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753418	0.87[MEX][hapmap]
rs10799337	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915952	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10915953	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10915954	0.88[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12032630	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047894	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12136759	0.83[MEX][hapmap]
rs1361559	0.81[CHB][hapmap]
rs2306119	0.87[MEX][hapmap]
rs2306121	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2889539	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3008192	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs3914142	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4653718	0.88[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653722	0.80[EUR][1000 genomes]
rs7367845	0.87[MEX][hapmap]
rs9286997	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9286998	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9286999	0.87[MEX][hapmap]
rs9629826	0.82[CHB][hapmap];0.87[MEX][hapmap]
rs9659225	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9660696	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9660874	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9660924	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9661836	0.88[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9662709	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9725308	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9725342	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9728014	0.85[EUR][1000 genomes]
rs9728310	0.88[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs9729232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9729554	0.86[AMR][1000 genomes];0.85[EUR][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	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv945331	chr1:226374378-226377514	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
4	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10799340	ACBD3	cis	normal skin	skin_eQTL
rs10799340	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs10799340	PARP1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226372600-226375400	Active TSS	GM12878-XiMat	blood
2	chr1:226372800-226375400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:226373400-226375400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:226373400-226375400	Active TSS	Hela-S3	cervix
5	chr1:226373600-226375400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:226373600-226375400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:226374600-226375400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr1:226374600-226375400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:226374600-226375400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:226374800-226375400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:226374800-226375400	Flanking Active TSS	Fetal Lung	lung
12	chr1:226374800-226375400	Flanking Active TSS	Dnd41	blood
13	chr1:226375000-226375400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:226375000-226375400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:226375000-226375400	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:226375000-226375600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:226375000-226380000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:226375000-226382600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:226375200-226375400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:226375200-226375400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:226375200-226375400	Enhancers	Primary B cells from cord blood	blood
22	chr1:226375200-226375400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:226375200-226375400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:226375200-226375400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:226375200-226375400	Enhancers	Adipose Nuclei	Adipose
26	chr1:226375200-226375400	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:226375200-226375400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr1:226375200-226375400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:226375200-226375400	Enhancers	HepG2	liver
30	chr1:226375200-226377200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:226375200-226377200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:226375200-226378000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:226375200-226411000	Weak transcription	Right Atrium	heart

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