Variant report

Variant	rs73862419
Chromosome Location	chr3:99975931-99975932
allele	G/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	GATA3	chr3:99975392-99976295	SK-N-SH	brain:	n/a	chr3:99975825-99975841
2	GATA3	chr3:99975480-99976224	SK-N-SH	brain:	n/a	chr3:99975825-99975841
3	PBX3	chr3:99975477-99976159	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr3:99975374-99976321	SK-N-SH	brain:	n/a	n/a
5	EP300	chr3:99975554-99976051	SK-N-SH_RA	brain:	n/a	chr3:99975724-99975734
6	TCF12	chr3:99975462-99976271	SK-N-SH	brain:	n/a	n/a
7	EP300	chr3:99975601-99976081	SK-N-SH_RA	brain:	n/a	chr3:99975724-99975734
8	NFIC	chr3:99975446-99976105	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:99975552-99976093	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:99975714-99975944	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:99975742-99976056	SK-N-MC	brain:	n/a	n/a
12	EP300	chr3:99975389-99976155	SK-N-SH	brain:	n/a	chr3:99975515-99975524 chr3:99975724-99975734
13	GATA2	chr3:99975759-99976043	SH-SY5Y	brain:	n/a	chr3:99975825-99975841
14	GATA3	chr3:99975716-99976092	SH-SY5Y	brain:	n/a	chr3:99975825-99975841
15	PBX3	chr3:99975499-99976086	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:99973186..99976114-chr3:99977290..99980794,4	K562	blood:
2	chr3:99971442..99977426-chr3:99977772..99982553,8	MCF-7	breast:
3	chr3:99974835..99977676-chr3:100052303..100055041,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16842137	1.00[AMR][1000 genomes]
rs403858	1.00[AMR][1000 genomes]
rs55721822	1.00[AMR][1000 genomes]
rs55978866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56186146	1.00[AMR][1000 genomes]
rs56227134	1.00[AMR][1000 genomes]
rs56678433	1.00[AMR][1000 genomes]
rs58283662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58869093	1.00[AMR][1000 genomes]
rs58953554	1.00[AMR][1000 genomes]
rs59674041	1.00[AMR][1000 genomes]
rs62636639	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6441136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6441243	1.00[AMR][1000 genomes]
rs6783067	1.00[AMR][1000 genomes]
rs6788019	1.00[AMR][1000 genomes]
rs6788854	1.00[AMR][1000 genomes]
rs6788875	1.00[AMR][1000 genomes]
rs73859919	1.00[AMR][1000 genomes]
rs73859921	1.00[AMR][1000 genomes]
rs73859924	1.00[AMR][1000 genomes]
rs73859931	1.00[AMR][1000 genomes]
rs73862437	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862445	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73862453	1.00[AMR][1000 genomes]
rs7630901	1.00[AMR][1000 genomes]
rs7652753	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99964600-99978600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:99964800-99979000	Weak transcription	Aorta	Aorta
3	chr3:99965200-99978800	Weak transcription	NH-A	brain
4	chr3:99965600-99978800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:99966600-99979000	Weak transcription	Gastric	stomach
6	chr3:99968000-99978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:99972800-99976200	Weak transcription	K562	blood
8	chr3:99973000-99978800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:99973400-99976200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:99973400-99978400	Weak transcription	Fetal Stomach	stomach
11	chr3:99973400-99978800	Weak transcription	Brain Substantia Nigra	brain
12	chr3:99973400-99978800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:99973400-99979000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:99973400-99979000	Weak transcription	Left Ventricle	heart
15	chr3:99973400-99979000	Weak transcription	HSMM	muscle
16	chr3:99973600-99976200	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:99973600-99976600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:99973600-99978200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:99973600-99978800	Weak transcription	HSMMtube	muscle
20	chr3:99973800-99978800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:99974000-99976200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:99974000-99978400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:99974200-99977000	Enhancers	HepG2	liver
24	chr3:99975200-99977000	Enhancers	Adipose Nuclei	Adipose
25	chr3:99975200-99977200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:99975400-99976000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:99975400-99976800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:99975400-99976800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:99975400-99976800	Enhancers	NHLF	lung
30	chr3:99975400-99977000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:99975400-99977200	Enhancers	Osteobl	bone
32	chr3:99975600-99976000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:99975600-99976000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:99975600-99978600	Weak transcription	Fetal Lung	lung
35	chr3:99975800-99976000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:99975800-99976200	Enhancers	NHDF-Ad	bronchial
37	chr3:99975800-99976800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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