Variant report

Variant	rs9310064
Chromosome Location	chr3:88107850-88107851
allele	G/T
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	MAX	chr3:88107534-88108810	SK-N-SH	brain:	n/a	n/a
2	CHD2	chr3:88107804-88108534	HepG2	liver:	n/a	n/a
3	POU2F2	chr3:88107773-88108163	GM12891	blood:	n/a	n/a
4	RFX5	chr3:88107774-88108888	GM12878	blood:	n/a	chr3:88108175-88108184
5	CTCF	chr3:88107720-88107870	SK-N-SH_RA	brain:	n/a	n/a
6	SP1	chr3:88107652-88109023	HCT-116	colon:	n/a	chr3:88107868-88107877 chr3:88107869-88107878 chr3:88107868-88107877 chr3:88108370-88108384 chr3:88108303-88108313 chr3:88108818-88108827 chr3:88108817-88108829 chr3:88108819-88108828 chr3:88108312-88108324 chr3:88107868-88107878 chr3:88108817-88108829 chr3:88107868-88107878 chr3:88107838-88107852 chr3:88108312-88108324 chr3:88108819-88108828 chr3:88107867-88107879 chr3:88108814-88108828 chr3:88107867-88107879 chr3:88108363-88108377
7	POLR2A	chr3:88107121-88108656	SK-N-MC	brain:	n/a	n/a
8	EP300	chr3:88107841-88108319	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr3:88107520-88108945	A549	lung:	n/a	n/a
10	POLR2A	chr3:88107501-88109036	HL-60	blood:	n/a	n/a
11	POLR2A	chr3:88107764-88108604	HCT-116	colon:	n/a	n/a
12	SP1	chr3:88107629-88108745	A549	lung:	n/a	chr3:88107868-88107877 chr3:88107869-88107878 chr3:88107868-88107877 chr3:88108370-88108384 chr3:88108303-88108313 chr3:88108312-88108324 chr3:88107868-88107878 chr3:88107868-88107878 chr3:88107838-88107852 chr3:88108312-88108324 chr3:88107867-88107879 chr3:88107867-88107879 chr3:88108363-88108377
13	POLR2A	chr3:88107614-88108698	K562	blood:	n/a	n/a
14	BHLHE40	chr3:88107318-88108662	GM12878	blood:	n/a	chr3:88108420-88108436 chr3:88107802-88107818 chr3:88107790-88107806 chr3:88108419-88108435
15	YY1	chr3:88107167-88108333	GM12891	blood:	n/a	chr3:88107603-88107612 chr3:88107607-88107618 chr3:88107869-88107878 chr3:88107802-88107811 chr3:88107606-88107615
16	POLR2A	chr3:88107379-88108940	NB4	blood:	n/a	n/a
17	POLR2A	chr3:88107302-88108568	GM12892	blood:	n/a	n/a
18	POLR2A	chr3:88107231-88108808	HUVEC	blood vessel:	n/a	n/a
19	GABPA	chr3:88107636-88108640	HL-60	blood:	n/a	chr3:88107869-88107878
20	MYC	chr3:88107621-88108898	MCF-7	breast:	n/a	n/a
21	SIN3AK20	chr3:88107649-88108027	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr3:88107631-88108684	GM12891	blood:	n/a	n/a
23	ZKSCAN1	chr3:88107698-88108589	Hela-S3	cervix:	n/a	n/a
24	MAZ	chr3:88106929-88109214	IMR90	lung:	n/a	n/a
25	FOXP2	chr3:88107598-88107995	SK-N-MC	brain:	n/a	n/a
26	FOXM1	chr3:88107619-88108749	GM12878	blood:	n/a	n/a
27	YY1	chr3:88107596-88108719	SK-N-SH_RA	brain:	n/a	chr3:88107603-88107612 chr3:88108420-88108429 chr3:88108424-88108435 chr3:88107607-88107618 chr3:88107869-88107878 chr3:88108423-88108432 chr3:88108420-88108434 chr3:88108421-88108432 chr3:88107802-88107811 chr3:88107606-88107615 chr3:88108426-88108435
28	ELF1	chr3:88107664-88108635	K562	blood:	n/a	chr3:88108420-88108429 chr3:88107803-88107815 chr3:88108321-88108330 chr3:88108421-88108433 chr3:88108426-88108435 chr3:88107802-88107811 chr3:88108423-88108432 chr3:88108320-88108331
29	POLR2A	chr3:88107594-88108936	H1-neurons	neurons:	n/a	n/a
30	ELK1	chr3:88107816-88108728	GM12878	blood:	n/a	chr3:88108322-88108331 chr3:88108322-88108331
31	SIN3AK20	chr3:88107650-88107999	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr3:88107202-88109029	IMR90	lung:	n/a	n/a
33	TBP	chr3:88107741-88108966	H1-hESC	embryonic stem cell:	n/a	n/a
34	ELF1	chr3:88107663-88108729	MCF-7	breast:	n/a	chr3:88108420-88108429 chr3:88107803-88107815 chr3:88108321-88108330 chr3:88108421-88108433 chr3:88108426-88108435 chr3:88107802-88107811 chr3:88108423-88108432 chr3:88108320-88108331
35	POLR2A	chr3:88107255-88109214	Raji	blood:	n/a	n/a
36	POLR2A	chr3:88107250-88108854	HL-60	blood:	n/a	n/a
37	BRCA1	chr3:88107691-88108406	GM12878	blood:	n/a	n/a
38	STAT1	chr3:88107753-88109563	GM12878	blood:	n/a	chr3:88107864-88107876 chr3:88107842-88107850 chr3:88109041-88109053
39	TCF7L2	chr3:88107558-88108982	HCT-116	colon:	n/a	n/a
40	CHD1	chr3:88107668-88108780	GM12878	blood:	n/a	n/a
41	MAX	chr3:88107329-88109357	NB4	blood:	n/a	n/a
42	CHD2	chr3:88107275-88109043	H1-hESC	embryonic stem cell:	n/a	chr3:88108819-88108829
43	POLR2A	chr3:88107432-88108651	K562	blood:	n/a	n/a
44	UBTF	chr3:88107344-88109457	K562	blood:	n/a	n/a
45	BHLHE40	chr3:88107694-88108985	K562	blood:	n/a	chr3:88108420-88108436 chr3:88107802-88107818 chr3:88107790-88107806 chr3:88108419-88108435
46	POLR2A	chr3:88107638-88108917	SK-N-SH	brain:	n/a	n/a
47	E2F6	chr3:88107631-88108879	K562	blood:	n/a	chr3:88108818-88108830 chr3:88108421-88108431 chr3:88108424-88108434 chr3:88107786-88107796 chr3:88108818-88108827 chr3:88107869-88107878
48	TBL1XR1	chr3:88107736-88108779	K562	blood:	n/a	n/a
49	MTA3	chr3:88106856-88109149	GM12878	blood:	n/a	n/a
50	CTCF	chr3:88107840-88107990	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:88107595..88108411-chr7:23571154..23571706,2	NB4	blood:
2	chr3:88090636..88092766-chr3:88106492..88108052,2	MCF-7	breast:
3	chr3:88107215..88109971-chr3:88197433..88199191,2	K562	blood:
4	chr3:88105942..88108461-chr3:88204357..88206943,2	K562	blood:
5	chr3:88106502..88110909-chr3:88195834..88201659,8	MCF-7	breast:
6	chr3:88104745..88109799-chr3:88197543..88201780,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229729	TF binding region
CGGBP1	TF binding region
ENSG00000164548	Chromatin interaction
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12632860	1.00[ASN][1000 genomes]
rs1367615	0.84[AFR][1000 genomes]
rs1431154	1.00[ASN][1000 genomes]
rs1431155	1.00[ASN][1000 genomes]
rs1431156	1.00[ASN][1000 genomes]
rs1469570	1.00[ASN][1000 genomes]
rs1594453	1.00[ASN][1000 genomes]
rs1594455	1.00[ASN][1000 genomes]
rs1604700	1.00[ASN][1000 genomes]
rs1835544	1.00[ASN][1000 genomes]
rs1897238	1.00[ASN][1000 genomes]
rs2033390	1.00[ASN][1000 genomes]
rs2344183	1.00[ASN][1000 genomes]
rs2344184	1.00[ASN][1000 genomes]
rs2567037	0.81[AFR][1000 genomes]
rs2735557	0.85[AFR][1000 genomes]
rs2880793	1.00[ASN][1000 genomes]
rs4241549	0.86[AFR][1000 genomes]
rs4241550	0.86[AFR][1000 genomes]
rs4303891	1.00[AMR][1000 genomes]
rs4404474	0.83[AFR][1000 genomes]
rs4425287	0.89[AFR][1000 genomes]
rs4431134	1.00[ASN][1000 genomes]
rs4515075	1.00[ASN][1000 genomes]
rs4616669	1.00[ASN][1000 genomes]
rs4858927	1.00[ASN][1000 genomes]
rs4858970	1.00[ASN][1000 genomes]
rs4858987	0.81[AFR][1000 genomes]
rs4858988	0.82[AFR][1000 genomes]
rs4858989	0.86[AFR][1000 genomes]
rs6767497	1.00[ASN][1000 genomes]
rs7650749	1.00[ASN][1000 genomes]
rs930154	1.00[ASN][1000 genomes]
rs930155	1.00[ASN][1000 genomes]
rs9310062	1.00[ASN][1000 genomes]
rs9310063	1.00[ASN][1000 genomes]
rs9812903	1.00[ASN][1000 genomes]
rs9833231	1.00[ASN][1000 genomes]
rs9850550	1.00[ASN][1000 genomes]
rs9854250	1.00[ASN][1000 genomes]
rs9864564	0.86[AFR][1000 genomes]
rs9867614	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr3:88106200-88108600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:88106200-88110400	Active TSS	HSMMtube	muscle
3	chr3:88106400-88110000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:88106400-88110000	Active TSS	Thymus	Thymus
5	chr3:88106400-88110400	Active TSS	HMEC	breast
6	chr3:88106400-88111400	Active TSS	NHLF	lung
7	chr3:88106400-88111600	Active TSS	Right Atrium	heart
8	chr3:88106600-88109600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:88106600-88109600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:88106600-88110000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:88106600-88110000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:88106600-88110400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:88106600-88111200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:88106600-88111200	Active TSS	K562	blood
15	chr3:88106800-88108400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:88106800-88108600	Active TSS	Brain Germinal Matrix	brain
17	chr3:88106800-88109000	Active TSS	Primary T cells fromperipheralblood	blood
18	chr3:88106800-88109200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:88106800-88109400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr3:88106800-88109400	Active TSS	Brain Anterior Caudate	brain
21	chr3:88106800-88109400	Active TSS	Colon Smooth Muscle	Colon
22	chr3:88106800-88109400	Active TSS	Placenta Amnion	Placenta Amnion
23	chr3:88106800-88109400	Active TSS	Stomach Mucosa	stomach
24	chr3:88106800-88109600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:88106800-88109600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:88106800-88109600	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:88106800-88109600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr3:88106800-88109600	Active TSS	Fetal Intestine Small	intestine
29	chr3:88106800-88109600	Active TSS	A549	lung
30	chr3:88106800-88109600	Active TSS	HUVEC	blood vessel
31	chr3:88106800-88109800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr3:88106800-88109800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:88106800-88109800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:88106800-88109800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:88106800-88109800	Active TSS	Hela-S3	cervix
36	chr3:88106800-88110000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:88106800-88110000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:88106800-88110000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:88106800-88110000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:88106800-88110000	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:88106800-88110000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:88106800-88110000	Active TSS	Colonic Mucosa	Colon
43	chr3:88106800-88110000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:88106800-88110000	Active TSS	Fetal Muscle Leg	muscle
45	chr3:88106800-88110000	Active TSS	Fetal Stomach	stomach
46	chr3:88106800-88110000	Active TSS	Fetal Thymus	thymus
47	chr3:88106800-88110000	Active TSS	Right Ventricle	heart
48	chr3:88106800-88110200	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:88106800-88110200	Active TSS	NH-A	brain
50	chr3:88106800-88111000	Active TSS	NHDF-Ad	bronchial

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