Variant report

Variant	rs9880179
Chromosome Location	chr3:98621133-98621134
allele	C/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	FOSL2	chr3:98620719-98621687	A549	lung:	n/a	n/a
2	KAP1	chr3:98620764-98621483	U2OS	brain:	n/a	n/a
3	SMC3	chr3:98620659-98621254	Hela-S3	cervix:	n/a	n/a
4	TAF1	chr3:98620116-98621139	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:98620089-98621148	HUVEC	blood vessel:	n/a	n/a
6	MAZ	chr3:98619241-98621681	IMR90	lung:	n/a	n/a
7	IRF1	chr3:98620319-98621133	K562	blood:	n/a	chr3:98620770-98620784 chr3:98620574-98620588
8	CHD2	chr3:98620168-98621338	HepG2	liver:	n/a	chr3:98620361-98620371
9	GABPA	chr3:98620509-98621310	MCF-7	breast:	n/a	n/a
10	EP300	chr3:98619783-98621301	SK-N-SH	brain:	n/a	chr3:98620499-98620515 chr3:98620885-98620892 chr3:98621042-98621056
11	MAX	chr3:98619724-98621179	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:98620258-98621168	PANC-1	pancreas:	n/a	n/a
13	REST	chr3:98619564-98621432	H1-neurons	neurons:	n/a	chr3:98620358-98620368
14	TAF1	chr3:98619078-98621229	A549	lung:	n/a	n/a
15	MAX	chr3:98619785-98621388	MCF-7	breast:	n/a	n/a
16	E2F6	chr3:98620149-98621214	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:98619780-98621155	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYBL2	chr3:98620688-98621166	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:98620223-98621195	SK-N-MC	brain:	n/a	n/a
20	SP1	chr3:98620453-98621151	H1-hESC	embryonic stem cell:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98620577-98620587 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620772-98620784 chr3:98620577-98620587
21	GATA2	chr3:98619874-98621719	SH-SY5Y	brain:	n/a	chr3:98621157-98621168
22	RCOR1	chr3:98619861-98621540	K562	blood:	n/a	n/a
23	REST	chr3:98619641-98621253	A549	lung:	n/a	chr3:98620358-98620368
24	HA-E2F1	chr3:98619690-98621251	MCF-7	breast:	n/a	chr3:98619867-98619876
25	POLR2A	chr3:98619772-98621198	GM12892	blood:	n/a	n/a
26	SP1	chr3:98619263-98621521	HCT-116	colon:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98621186-98621196 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98621186-98621195 chr3:98620577-98620587 chr3:98621182-98621196 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620392-98620401 chr3:98620772-98620784 chr3:98620577-98620587
27	PBX3	chr3:98619748-98621422	SK-N-SH	brain:	n/a	n/a
28	RCOR1	chr3:98619923-98621359	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:98620205-98621238	HL-60	blood:	n/a	n/a
30	POLR2A	chr3:98619880-98621195	K562	blood:	n/a	n/a
31	POLR2A	chr3:98619668-98621142	ECC-1	luminal epithelium:	n/a	n/a
32	GATA3	chr3:98619677-98621668	A549	lung:	n/a	chr3:98621157-98621168
33	MAZ	chr3:98619882-98621214	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:98619740-98621167	H1-neurons	neurons:	n/a	n/a
35	SP1	chr3:98619734-98621187	A549	lung:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98620577-98620587 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620392-98620401 chr3:98620772-98620784 chr3:98620577-98620587
36	HCFC1	chr3:98620288-98621246	Hela-S3	cervix:	n/a	n/a
37	RCOR1	chr3:98620316-98621523	K562	blood:	n/a	n/a
38	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
39	POLR2A	chr3:98619774-98621183	MCF-7	breast:	n/a	n/a
40	POLR2A	chr3:98619057-98621173	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr3:98619206-98621801	HCT-116	colon:	n/a	n/a
42	NFIC	chr3:98619473-98621196	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr3:98619778-98621367	Hela-S3	cervix:	n/a	n/a
44	FOXM1	chr3:98620337-98621273	GM12878	blood:	n/a	n/a
45	TBP	chr3:98620082-98621287	HepG2	liver:	n/a	n/a
46	HCFC1	chr3:98619882-98621307	K562	blood:	n/a	n/a
47	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
48	MAX	chr3:98619796-98621202	SK-N-SH	brain:	n/a	n/a
49	MAX	chr3:98619613-98621634	A549	lung:	n/a	n/a
50	POLR2A	chr3:98618341-98621471	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region
ENSG00000207331	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935513	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935514	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12632798	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12636683	0.84[AMR][1000 genomes]
rs12695786	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13071075	0.88[AMR][1000 genomes]
rs13081543	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13316760	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13319666	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371687	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1383906	0.83[EUR][1000 genomes]
rs1383907	0.83[EUR][1000 genomes]
rs2062058	0.85[ASN][1000 genomes]
rs2333923	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2340794	0.80[EUR][1000 genomes]
rs2439237	0.82[ASN][1000 genomes]
rs2449046	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2470853	0.85[ASN][1000 genomes]
rs2470855	0.85[ASN][1000 genomes]
rs2470870	0.85[ASN][1000 genomes]
rs2470872	0.86[ASN][1000 genomes]
rs2470873	0.83[EUR][1000 genomes]
rs2470877	0.83[EUR][1000 genomes]
rs2470880	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs278379	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35483904	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35760367	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35936923	0.83[EUR][1000 genomes]
rs4546099	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577404	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4857415	0.84[AMR][1000 genomes]
rs6767370	0.86[AMR][1000 genomes]
rs6774875	0.85[ASN][1000 genomes]
rs6791389	0.85[AMR][1000 genomes]
rs7615628	0.85[ASN][1000 genomes]
rs7615856	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828614	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs828617	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs828621	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs870202	0.85[ASN][1000 genomes]
rs955351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682876	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837206	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9842522	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9880179	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs9880179	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98615600-98621200	Active TSS	NHLF	lung
2	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
4	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
6	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:98618400-98621200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:98618400-98621200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:98618400-98621200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:98618400-98621200	Active TSS	Fetal Kidney	kidney
12	chr3:98618400-98621200	Active TSS	GM12878-XiMat	blood
13	chr3:98618400-98621400	Active TSS	Left Ventricle	heart
14	chr3:98618400-98621600	Active TSS	Right Atrium	heart
15	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:98618600-98621200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:98618600-98621400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:98618600-98621600	Active TSS	Ovary	ovary
19	chr3:98618600-98621800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:98618600-98621800	Active TSS	HSMMtube	muscle
21	chr3:98618800-98621200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:98618800-98621200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:98618800-98621200	Active TSS	Stomach Smooth Muscle	stomach
24	chr3:98618800-98621400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:98618800-98621600	Active TSS	Psoas Muscle	Psoas
26	chr3:98618800-98621800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:98618800-98622200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:98619000-98621200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:98619000-98621200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:98619000-98621200	Active TSS	HSMM	muscle
31	chr3:98619000-98621600	Active TSS	Fetal Muscle Trunk	muscle
32	chr3:98619200-98621200	Active TSS	Brain Substantia Nigra	brain
33	chr3:98619200-98621200	Active TSS	HMEC	breast
34	chr3:98619200-98621200	Active TSS	K562	blood
35	chr3:98619200-98621400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr3:98619200-98621600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr3:98619200-98621600	Active TSS	Aorta	Aorta
38	chr3:98619400-98621200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:98619400-98621200	Active TSS	Fetal Lung	lung
40	chr3:98619400-98621200	Active TSS	Lung	lung
41	chr3:98619400-98621200	Active TSS	A549	lung
42	chr3:98619400-98621400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:98619400-98621400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:98619400-98621400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:98619400-98621600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:98619600-98621200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:98619600-98621200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:98619600-98621200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:98619600-98621200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:98619600-98621200	Active TSS	Brain Cingulate Gyrus	brain

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