Variant report

Variant	rs2305632
Chromosome Location	chr3:47042713-47042714
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	chr3:47041924-47042868	K562	blood:	n/a	n/a
2	POLR2A	chr3:47042702-47043062	K562	blood:	n/a	n/a
3	POLR2A	chr3:47042706-47043175	K562	blood:	n/a	n/a
4	POLR2A	chr3:47042294-47043188	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:47042260-47043327	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:47042255-47042714	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:47042304-47042781	HL-60	blood:	n/a	n/a
8	POLR2A	chr3:47042287-47043216	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47019689..47022693-chr3:47040941..47043835,3	MCF-7	breast:
2	chr3:46929621..46931545-chr3:47041151..47042840,2	K562	blood:
3	chr3:47042301..47045391-chr3:47048299..47050590,3	MCF-7	breast:

Variant related genes	Relation type
NBEAL2	TF binding region
ENSG00000160799	Chromatin interaction
ENSG00000268537	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12485582	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486248	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489851	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491419	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497141	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17079425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305640	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201996	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3816531	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60285825	0.87[AMR][1000 genomes]
rs61364027	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7372834	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised 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	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
2	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:47029800-47050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47030200-47044600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:47030800-47045600	Weak transcription	Aorta	Aorta
6	chr3:47031000-47049600	Strong transcription	Gastric	stomach
7	chr3:47031000-47050200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:47031000-47053000	Strong transcription	Dnd41	blood
9	chr3:47031800-47043400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:47032200-47050000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:47033800-47049200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:47034200-47049800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:47035400-47049000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:47036800-47044200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:47037400-47042800	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr3:47037400-47043000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:47038000-47050000	Strong transcription	Thymus	Thymus
18	chr3:47038600-47044400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:47038600-47044600	Strong transcription	K562	blood
20	chr3:47038600-47050000	Strong transcription	Fetal Stomach	stomach
21	chr3:47038600-47050400	Weak transcription	Fetal Lung	lung
22	chr3:47039000-47050000	Strong transcription	Adipose Nuclei	Adipose
23	chr3:47039600-47042800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:47039800-47050200	Strong transcription	Colonic Mucosa	Colon
25	chr3:47039800-47058000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:47040000-47042800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:47040000-47043600	Strong transcription	GM12878-XiMat	blood
28	chr3:47040000-47049400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:47040000-47050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:47040200-47043600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:47040200-47043600	Strong transcription	Placenta	Placenta
32	chr3:47040200-47046000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:47040200-47049000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:47040200-47049000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:47040200-47049800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:47040200-47049800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:47040400-47046400	Strong transcription	Ovary	ovary
38	chr3:47040400-47048800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:47040400-47049200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:47040400-47049600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:47040400-47050000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:47040400-47050000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:47040400-47050000	Strong transcription	Spleen	Spleen
44	chr3:47040400-47050400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:47040400-47050400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:47040400-47050400	Weak transcription	Right Atrium	heart
47	chr3:47040600-47043400	Strong transcription	Pancreas	Pancrea
48	chr3:47040600-47043800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:47040600-47048000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:47040600-47048200	Strong transcription	Primary B cells from peripheral blood	blood

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