Variant report

Variant	rs293816
Chromosome Location	chr3:191074245-191074246
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	chr3:191074168-191075053	MCF10A-Er-Src	breast:	n/a	n/a
2	TEAD4	chr3:191074215-191074737	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:191073947-191075439	PFSK-1	brain:	n/a	n/a
4	TEAD4	chr3:191074199-191074919	ECC-1	luminal epithelium:	n/a	n/a
5	EBF1	chr3:191073206-191074715	GM12878	blood:	n/a	chr3:191074290-191074299 chr3:191074290-191074299 chr3:191074288-191074301
6	EP300	chr3:191074122-191074965	ECC-1	luminal epithelium:	n/a	chr3:191074757-191074764
7	WRNIP1	chr3:191073196-191074259	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191059352..191062066-chr3:191073918..191075676,3	K562	blood:
2	chr3:191059352..191066044-chr3:191070268..191075568,9	K562	blood:

Variant related genes	Relation type
CCDC50	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1066857	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061649	0.90[ASN][1000 genomes]
rs150505	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520200	0.84[ASN][1000 genomes]
rs1656143	0.90[ASN][1000 genomes]
rs1662184	0.90[ASN][1000 genomes]
rs167148	0.90[ASN][1000 genomes]
rs1715641	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176821	0.90[ASN][1000 genomes]
rs176822	0.88[ASN][1000 genomes]
rs184140	0.90[ASN][1000 genomes]
rs1850961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186064	0.90[ASN][1000 genomes]
rs186065	0.90[ASN][1000 genomes]
rs186068	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211043	0.90[ASN][1000 genomes]
rs2572064	0.90[ASN][1000 genomes]
rs293807	0.90[ASN][1000 genomes]
rs293809	0.90[ASN][1000 genomes]
rs293810	0.90[ASN][1000 genomes]
rs293811	0.90[ASN][1000 genomes]
rs293812	0.90[ASN][1000 genomes]
rs293813	0.90[ASN][1000 genomes]
rs293814	0.90[ASN][1000 genomes]
rs293817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293837	0.90[ASN][1000 genomes]
rs293839	0.90[ASN][1000 genomes]
rs293840	0.90[ASN][1000 genomes]
rs293841	0.90[ASN][1000 genomes]
rs293852	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293854	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293856	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293857	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293858	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs293859	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs293861	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs364519	0.90[ASN][1000 genomes]
rs383529	0.90[ASN][1000 genomes]
rs386241	0.90[ASN][1000 genomes]
rs389765	0.90[ASN][1000 genomes]
rs392311	0.90[ASN][1000 genomes]
rs399575	0.90[ASN][1000 genomes]
rs403078	0.90[ASN][1000 genomes]
rs407226	0.90[ASN][1000 genomes]
rs415149	0.90[ASN][1000 genomes]
rs420266	0.90[ASN][1000 genomes]
rs423989	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs429374	0.90[ASN][1000 genomes]
rs429521	0.90[ASN][1000 genomes]
rs436393	0.90[ASN][1000 genomes]
rs436428	0.90[ASN][1000 genomes]
rs438589	0.90[ASN][1000 genomes]
rs440266	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs441509	0.90[ASN][1000 genomes]
rs445914	0.90[ASN][1000 genomes]
rs447931	0.90[ASN][1000 genomes]
rs449398	0.90[ASN][1000 genomes]
rs491252	0.90[ASN][1000 genomes]
rs497918	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513632	0.90[ASN][1000 genomes]
rs520494	0.90[ASN][1000 genomes]
rs520600	0.88[ASN][1000 genomes]
rs568702	0.87[ASN][1000 genomes]
rs578401	0.90[ASN][1000 genomes]
rs695910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696347	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs696348	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs696349	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs697913	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv508266	chr3:191064212-191083637	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1808657	chr3:191064330-191081793	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv878106	chr3:191064528-191081344	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1823184	chr3:191064803-191082303	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1848120	chr3:191064803-191082303	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1839532	chr3:191065921-191074873	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv592852	chr3:191073228-191093310	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv592853	chr3:191073228-191094985	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191050200-191074800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:191060600-191074800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:191062000-191075600	Weak transcription	K562	blood
4	chr3:191062200-191075400	Weak transcription	Fetal Brain Female	brain
5	chr3:191063000-191076600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:191068600-191074600	Weak transcription	Fetal Stomach	stomach
7	chr3:191068600-191075000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:191068600-191075000	Weak transcription	Aorta	Aorta
9	chr3:191068600-191076600	Weak transcription	Fetal Kidney	kidney
10	chr3:191068800-191075400	Enhancers	Colon Smooth Muscle	Colon
11	chr3:191068800-191078800	Weak transcription	Fetal Brain Male	brain
12	chr3:191069400-191075000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:191071000-191074800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:191071000-191076000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:191071200-191076800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:191071200-191078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:191071200-191078800	Weak transcription	Lung	lung
20	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
21	chr3:191071400-191074400	Weak transcription	Stomach Mucosa	stomach
22	chr3:191071400-191074800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:191071400-191075000	Weak transcription	Fetal Lung	lung
24	chr3:191071400-191075800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:191071400-191078400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:191071400-191078800	Weak transcription	Gastric	stomach
27	chr3:191071400-191078800	Weak transcription	Pancreas	Pancrea
28	chr3:191071400-191078800	Weak transcription	Spleen	Spleen
29	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
30	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:191071600-191074400	Weak transcription	A549	lung
33	chr3:191071800-191074400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:191071800-191074400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:191071800-191075000	Enhancers	Liver	Liver
36	chr3:191072200-191075600	Weak transcription	Fetal Intestine Large	intestine
37	chr3:191072400-191076400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:191072600-191075800	Weak transcription	Brain Anterior Caudate	brain
39	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:191072800-191076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:191073000-191074400	Enhancers	Right Ventricle	heart
42	chr3:191073000-191074800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:191073200-191074400	Enhancers	Placenta	Placenta
44	chr3:191073200-191074400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:191073200-191074400	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:191073200-191074400	Enhancers	NHDF-Ad	bronchial
47	chr3:191073200-191074600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:191073200-191074800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:191073200-191075000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:191073200-191075000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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