Variant report

Variant	rs278378
Chromosome Location	chr3:98531446-98531447
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	chr3:98529600-98531559	U87	brain:	n/a	n/a
2	RAD21	chr3:98531400-98532194	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:98529555-98531559	U87	brain:	n/a	n/a
4	POLR2A	chr3:98530977-98539024	U87	brain:	n/a	n/a
5	FOXA2	chr3:98531319-98532119	HepG2	liver:	n/a	n/a
6	GATA1	chr3:98531319-98531707	PBDEFetal	blood:	n/a	n/a
7	POLR2A	chr3:98530971-98537862	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98311356..98313726-chr3:98530079..98532585,2	MCF-7	breast:
2	chr3:98315529..98316439-chr3:98531389..98532230,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.80[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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2173598	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278375	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs7373983	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.92[AFR][1000 genomes]
rs828619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
3	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
5	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
7	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:98523800-98533600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:98523800-98533800	Strong transcription	NHDF-Ad	bronchial
13	chr3:98523800-98535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:98524200-98544200	Strong transcription	HSMM	muscle
17	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
18	chr3:98526200-98543200	Weak transcription	Lung	lung
19	chr3:98526400-98532000	Weak transcription	Esophagus	oesophagus
20	chr3:98526400-98533600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:98526400-98535600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:98526400-98536000	Weak transcription	Aorta	Aorta
23	chr3:98526400-98538200	Weak transcription	GM12878-XiMat	blood
24	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
26	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
29	chr3:98526600-98533800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:98526600-98537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:98526600-98539000	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
33	chr3:98526800-98533000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:98527000-98533800	Strong transcription	Osteobl	bone
35	chr3:98527000-98535600	Weak transcription	Pancreas	Pancrea
36	chr3:98527000-98536600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:98527000-98536600	Weak transcription	K562	blood
38	chr3:98527000-98538600	Weak transcription	Primary T cells from cord blood	blood
39	chr3:98527200-98532400	Weak transcription	Ovary	ovary
40	chr3:98527200-98536600	Weak transcription	Brain Anterior Caudate	brain
41	chr3:98527200-98536600	Weak transcription	Brain Germinal Matrix	brain
42	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:98527600-98533800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:98528200-98533400	Weak transcription	Fetal Intestine Large	intestine
47	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:98528400-98534200	Strong transcription	HMEC	breast
49	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:98528600-98533600	Weak transcription	Left Ventricle	heart

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