Variant report

Variant	rs73838346
Chromosome Location	chr3:52334989-52334990
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	chr3:52327536-52335341	HepG2	liver:	n/a	n/a
2	EP300	chr3:52334689-52335003	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
4	REST	chr3:52334824-52335090	K562	blood:	n/a	n/a
5	TEAD4	chr3:52333972-52335041	K562	blood:	n/a	n/a
6	EGR1	chr3:52334843-52335022	K562	blood:	n/a	n/a
7	CUX1	chr3:52334139-52335042	K562	blood:	n/a	n/a
8	JUN	chr3:52333888-52335164	K562	blood:	n/a	chr3:52335096-52335105
9	JUND	chr3:52333872-52335486	SK-N-SH	brain:	n/a	chr3:52335096-52335105
10	ZBTB7A	chr3:52334972-52335178	K562	blood:	n/a	n/a
11	STAT5A	chr3:52334833-52335203	GM12878	blood:	n/a	n/a
12	JUND	chr3:52334039-52335065	K562	blood:	n/a	n/a
13	FOSL2	chr3:52334538-52335113	SK-N-SH	brain:	n/a	chr3:52335096-52335105

No.	Distal block	Cell Line	Cell type
1	chr3:52334853..52337240-chr3:52339091..52341115,3	K562	blood:
2	chr3:52334304..52337060-chr3:52343020..52346051,4	K562	blood:
3	chr3:52324601..52327389-chr3:52333831..52335599,2	MCF-7	breast:

Variant related genes	Relation type
GLYCTK-AS1	TF binding region
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55931436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56263308	1.00[AMR][1000 genomes]
rs56332579	1.00[AMR][1000 genomes]
rs57265663	1.00[AMR][1000 genomes]
rs60063053	1.00[AMR][1000 genomes]
rs61589587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61738522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765965	1.00[AMR][1000 genomes]
rs6778451	1.00[AMR][1000 genomes]
rs6789826	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835708	1.00[AMR][1000 genomes]
rs73835711	1.00[AMR][1000 genomes]
rs73835763	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835767	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835771	0.87[AFR][1000 genomes]
rs73835772	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835773	1.00[AMR][1000 genomes]
rs73835774	1.00[AMR][1000 genomes]
rs73837050	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73837056	1.00[AMR][1000 genomes]
rs73837058	1.00[AMR][1000 genomes]
rs73837574	1.00[AMR][1000 genomes]
rs73838349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7644241	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers 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	45 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	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
2	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
4	chr3:52327400-52338400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:52328000-52337000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:52328200-52340200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
11	chr3:52328600-52340000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:52328800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:52330000-52335000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:52330200-52343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:52330200-52343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:52331000-52337600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:52331000-52343200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:52331200-52335200	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:52331200-52342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:52331400-52336400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:52331600-52335200	Enhancers	Stomach Mucosa	stomach
26	chr3:52331800-52335600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:52332000-52335200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr3:52332000-52335200	Enhancers	Placenta	Placenta
29	chr3:52332200-52335200	Enhancers	Lung	lung
30	chr3:52332400-52335200	Enhancers	Right Ventricle	heart
31	chr3:52332600-52335200	Enhancers	Fetal Heart	heart
32	chr3:52332600-52335200	Enhancers	Left Ventricle	heart
33	chr3:52332600-52335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:52332600-52335600	Bivalent Enhancer	Fetal Brain Male	brain
35	chr3:52332800-52335200	Enhancers	NH-A	brain
36	chr3:52332800-52335400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:52333000-52335600	Enhancers	Fetal Muscle Leg	muscle
38	chr3:52333000-52340800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:52333000-52341200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
41	chr3:52333200-52335200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:52333200-52335200	Enhancers	HUVEC	blood vessel
43	chr3:52333200-52335400	Enhancers	Ovary	ovary
44	chr3:52333400-52335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:52333400-52335200	Enhancers	Fetal Stomach	stomach
46	chr3:52333400-52335400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:52333400-52335400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52333400-52335600	Enhancers	Fetal Intestine Large	intestine
49	chr3:52333400-52335600	Enhancers	Fetal Intestine Small	intestine
50	chr3:52333400-52339200	Weak transcription	Colonic Mucosa	Colon

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