Variant report

Variant	rs2470883
Chromosome Location	chr3:98619052-98619053
allele	C/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	POLR2A	chr3:98618321-98620638	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr3:98618761-98619174	A549	lung:	n/a	n/a
3	MYC	chr3:98618500-98619417	MCF10A-Er-Src	breast:	n/a	n/a
4	BCL3	chr3:98618365-98619205	A549	lung:	n/a	n/a
5	POLR2A	chr3:98619004-98619308	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr3:98618295-98619513	A549	lung:	n/a	n/a
7	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
8	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
9	POLR2A	chr3:98618341-98621471	ProgFib	skin:	n/a	n/a
10	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
11	REST	chr3:98618368-98619272	A549	lung:	n/a	n/a
12	SIN3AK20	chr3:98618345-98619139	A549	lung:	n/a	n/a
13	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
14	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
15	MXI1	chr3:98618881-98621804	IMR90	lung:	n/a	n/a
16	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
17	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a
18	MYC	chr3:98618830-98619145	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	0.86[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.98[AFR][1000 genomes]
rs2173598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.84[AFR][1000 genomes]
rs2470828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.98[AFR][1000 genomes]
rs278375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929491	0.84[AFR][1000 genomes]
rs4273318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5013928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440189	0.81[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.95[AFR][1000 genomes]
rs7373983	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73858658	0.81[AFR][1000 genomes]
rs7626395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs974982	0.81[AFR][1000 genomes]
rs996199	0.98[AFR][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

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
4	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:98613600-98619400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:98614200-98619600	Weak transcription	Gastric	stomach
7	chr3:98615000-98619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:98615600-98619600	Flanking Active TSS	HUVEC	blood vessel
10	chr3:98615600-98621200	Active TSS	NHLF	lung
11	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
13	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
15	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:98618200-98619400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:98618200-98619400	Enhancers	Fetal Brain Male	brain
18	chr3:98618200-98619600	Transcr. at gene 5' and 3'	Osteobl	bone
19	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:98618400-98619200	Enhancers	Colon Smooth Muscle	Colon
21	chr3:98618400-98619200	Flanking Active TSS	HepG2	liver
22	chr3:98618400-98619400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:98618400-98619400	Transcr. at gene 5' and 3'	A549	lung
24	chr3:98618400-98619600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NH-A	brain
26	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NHEK	skin
27	chr3:98618400-98619800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:98618400-98619800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:98618400-98619800	Active TSS	Brain Germinal Matrix	brain
30	chr3:98618400-98619800	Flanking Active TSS	Fetal Brain Female	brain
31	chr3:98618400-98621200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr3:98618400-98621200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:98618400-98621200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:98618400-98621200	Active TSS	Fetal Kidney	kidney
35	chr3:98618400-98621200	Active TSS	GM12878-XiMat	blood
36	chr3:98618400-98621400	Active TSS	Left Ventricle	heart
37	chr3:98618400-98621600	Active TSS	Right Atrium	heart
38	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:98618600-98619200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:98618600-98619200	Transcr. at gene 5' and 3'	HMEC	breast
41	chr3:98618600-98619400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:98618600-98619400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:98618600-98619400	Active TSS	Fetal Muscle Leg	muscle
44	chr3:98618600-98619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:98618600-98619600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:98618600-98619600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:98618600-98619600	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:98618600-98619800	Flanking Active TSS	Dnd41	blood
49	chr3:98618600-98620000	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr3:98618600-98621200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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