Variant report

Variant	rs9863874
Chromosome Location	chr3:52266213-52266214
allele	A/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	POLR2A	chr3:52266143-52266521	HepG2	liver:	n/a	n/a
2	ELF1	chr3:52265473-52266451	GM12878	blood:	n/a	chr3:52265787-52265799

No.	Distal block	Cell Line	Cell type
1	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
2	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
3	chr3:52264055..52267306-chr3:52309351..52312799,8	MCF-7	breast:
4	chr3:52262375..52268246-chr3:52270366..52274345,8	K562	blood:

Variant related genes	Relation type
ENSG00000173366	TF binding region
ENSG00000243224	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[EUR][1000 genomes]
rs17052143	1.00[EUR][1000 genomes]
rs28413740	1.00[EUR][1000 genomes]
rs28434358	1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[EUR][1000 genomes]
rs9813489	1.00[EUR][1000 genomes]
rs9813653	1.00[EUR][1000 genomes]
rs9815559	1.00[EUR][1000 genomes]
rs9821916	1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[EUR][1000 genomes]
rs9834363	1.00[EUR][1000 genomes]
rs9836166	1.00[EUR][1000 genomes]
rs9842960	1.00[EUR][1000 genomes]
rs9843055	1.00[EUR][1000 genomes]
rs9844178	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9868332	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	esv3376719	chr3:52263462-52266260	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
3	chr3:52251600-52266600	Weak transcription	Psoas Muscle	Psoas
4	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
5	chr3:52255000-52268600	Weak transcription	Right Atrium	heart
6	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52259600-52268200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:52261000-52266600	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr3:52261000-52269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:52261200-52266400	Strong transcription	Lung	lung
11	chr3:52261200-52267000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
13	chr3:52261400-52269000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:52261400-52269600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:52261600-52266800	Strong transcription	Placenta	Placenta
16	chr3:52261600-52267000	Strong transcription	Gastric	stomach
17	chr3:52261600-52267200	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:52261600-52270600	Strong transcription	NHEK	skin
22	chr3:52261800-52266400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:52261800-52266800	Strong transcription	Fetal Brain Female	brain
24	chr3:52261800-52267200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:52261800-52267800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:52261800-52269400	Strong transcription	Brain Germinal Matrix	brain
27	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52261800-52270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:52262000-52269200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52262200-52267000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:52262400-52266600	Strong transcription	Aorta	Aorta
34	chr3:52262400-52269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:52262400-52269800	Strong transcription	Osteobl	bone
36	chr3:52262400-52270000	Strong transcription	NHLF	lung
37	chr3:52262800-52268600	Strong transcription	Ovary	ovary
38	chr3:52263000-52269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:52263200-52266800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:52263200-52269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52263600-52266600	Strong transcription	HSMM	muscle
42	chr3:52264200-52271400	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr3:52264600-52266800	Genic enhancers	Right Ventricle	heart
44	chr3:52264600-52270000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:52264800-52267800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:52264800-52270600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:52265000-52266400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:52265000-52269400	Weak transcription	Hela-S3	cervix
49	chr3:52265000-52270400	Weak transcription	K562	blood
50	chr3:52265000-52272000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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