Variant report

Variant	rs73088787
Chromosome Location	chr3:52313844-52313845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:52311125-52315006	SK-N-SH	brain:	n/a	chr3:52313881-52313895 chr3:52312475-52312484 chr3:52311546-52311555 chr3:52313068-52313082 chr3:52313069-52313083
2	POLR2A	chr3:52313827-52314658	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:52313731-52314163	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:52313795-52314504	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr3:52313596-52313940	U87	brain:	n/a	n/a
6	POLR2A	chr3:52313306-52314466	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr3:52310948-52314914	SK-N-SH	brain:	n/a	n/a
8	TBP	chr3:52313587-52313915	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:52313763-52314457	SK-N-MC	brain:	n/a	n/a
10	YY1	chr3:52313716-52314493	SK-N-SH_RA	brain:	n/a	n/a
11	GATA2	chr3:52313528-52314168	SH-SY5Y	brain:	n/a	n/a
12	POLR2A	chr3:52313823-52314302	HCT-116	colon:	n/a	n/a
13	GATA3	chr3:52313534-52313939	SH-SY5Y	brain:	n/a	n/a
14	POLR2A	chr3:52313756-52313855	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:28973386..28976212-chr3:52311138..52314136,3	K562	blood:
2	chr3:52312898..52314508-chr3:52316023..52317538,2	MCF-7	breast:
3	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
4	chr3:52278055..52281861-chr3:52310588..52314481,6	K562	blood:
5	chr3:52312964..52314575-chr3:52349556..52352232,2	K562	blood:
6	chr3:52312779..52315046-chr3:52326364..52328417,2	MCF-7	breast:
7	chr3:52297780..52305259-chr3:52310132..52314407,14	MCF-7	breast:
8	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
9	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
10	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
11	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:
12	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
13	chr3:52263787..52265921-chr3:52311180..52314270,4	MCF-7	breast:
14	chr3:52278055..52281861-chr3:52310505..52315451,9	K562	blood:
15	chr3:52270811..52274971-chr3:52310538..52315239,11	K562	blood:
16	chr3:52312722..52314589-chr3:52419579..52422419,2	MCF-7	breast:
17	chr3:52270811..52276588-chr3:52310648..52314131,11	K562	blood:
18	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYCTK-1	chr3:52312868-52315151	NONHSAT089909

No data

Variant related genes	Relation type
WDR82	TF binding region
ENSG00000239732	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000173366	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000199150	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000207926	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11707938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11720866	0.91[EUR][1000 genomes]
rs56296139	0.97[EUR][1000 genomes]
rs73088790	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52310200-52314000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:52310800-52314400	Active TSS	Stomach Smooth Muscle	stomach
3	chr3:52311000-52314000	Active TSS	NHLF	lung
4	chr3:52311000-52314400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:52311400-52314000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:52311400-52314000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:52311600-52314000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:52312800-52314200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr3:52312800-52314400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:52313000-52314000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:52313000-52314000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:52313000-52314000	Flanking Active TSS	Dnd41	blood
13	chr3:52313000-52314400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr3:52313200-52314000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:52313200-52314000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:52313200-52314000	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:52313200-52314000	Enhancers	Fetal Brain Male	brain
18	chr3:52313200-52314200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:52313200-52314200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr3:52313200-52314200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:52313200-52314200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:52313200-52314200	Enhancers	Liver	Liver
23	chr3:52313200-52314200	Flanking Active TSS	Fetal Lung	lung
24	chr3:52313200-52314400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:52313200-52314400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr3:52313200-52314400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:52313200-52314400	Flanking Active TSS	HUVEC	blood vessel
28	chr3:52313200-52314600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:52313200-52314600	Enhancers	Fetal Heart	heart
30	chr3:52313200-52314600	Enhancers	Stomach Mucosa	stomach
31	chr3:52313200-52321000	Weak transcription	Gastric	stomach
32	chr3:52313400-52314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52313400-52314000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52313400-52314000	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:52313400-52314000	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr3:52313400-52314000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr3:52313400-52314000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:52313400-52314000	Enhancers	Small Intestine	intestine
39	chr3:52313400-52314000	Flanking Active TSS	A549	lung
40	chr3:52313400-52314000	Flanking Active TSS	GM12878-XiMat	blood
41	chr3:52313400-52314200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:52313400-52314200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:52313400-52314200	Enhancers	Primary B cells from peripheral blood	blood
44	chr3:52313400-52314200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:52313400-52314200	Weak transcription	Right Ventricle	heart
46	chr3:52313400-52314200	Weak transcription	Spleen	Spleen
47	chr3:52313400-52314400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:52313400-52314400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:52313400-52314400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:52313400-52314400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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