Variant report

Variant	rs2464612
Chromosome Location	chr3:112284302-112284303
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	chr3:112284296-112284363	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112279902..112282989-chr3:112283976..112287292,5	MCF-7	breast:

Variant related genes	Relation type
ATG3	TF binding region
SLC35A5	TF binding region
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10934177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[ASN][1000 genomes]
rs1388442	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638041	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705554	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7618978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	1.00[ASN][1000 genomes]
rs971832	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:112281800-112287000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:112281800-112289800	Weak transcription	HSMMtube	muscle
4	chr3:112281800-112290400	Weak transcription	Lung	lung
5	chr3:112281800-112291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
7	chr3:112281800-112301600	Weak transcription	HepG2	liver
8	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
10	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
11	chr3:112281800-112325400	Weak transcription	Gastric	stomach
12	chr3:112282000-112285200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:112282000-112287200	Weak transcription	Aorta	Aorta
14	chr3:112282000-112288200	Weak transcription	Ovary	ovary
15	chr3:112282000-112289600	Weak transcription	Colonic Mucosa	Colon
16	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
19	chr3:112282200-112284400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:112282200-112284800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:112282200-112285200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:112282200-112286400	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:112282200-112287200	Weak transcription	HSMM	muscle
24	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
25	chr3:112282400-112284600	Enhancers	Fetal Intestine Large	intestine
26	chr3:112282400-112284600	Enhancers	Fetal Intestine Small	intestine
27	chr3:112282400-112286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:112282400-112286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:112282400-112287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:112282400-112287400	Weak transcription	NH-A	brain
31	chr3:112282400-112287400	Weak transcription	Osteobl	bone
32	chr3:112282400-112288200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:112282400-112289000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:112282400-112289200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:112282400-112289800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:112282400-112290400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:112282400-112290400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:112282400-112291200	Weak transcription	NHLF	lung
39	chr3:112282400-112291800	Weak transcription	Fetal Kidney	kidney
40	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach
41	chr3:112282400-112301600	Weak transcription	Hela-S3	cervix
42	chr3:112282400-112304400	Weak transcription	Fetal Heart	heart
43	chr3:112282400-112306600	Weak transcription	Right Ventricle	heart
44	chr3:112282400-112307200	Weak transcription	Small Intestine	intestine
45	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:112282600-112284400	Enhancers	Duodenum Mucosa	Duodenum

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