Variant report

Variant	rs1562277
Chromosome Location	chr2:113940280-113940281
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113940082-113940482	K562	blood:	n/a	n/a
2	POLR2A	chr2:113940197-113941011	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:113940162-113941185	GM19193	blood:	n/a	n/a
4	POLR2A	chr2:113940225-113941217	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:113940180-113940322	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:113938740-113941821	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:113939774-113941138	GM18505	blood:	n/a	n/a
8	POLR2A	chr2:113940207-113941619	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:113940135-113940807	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:113940167-113941692	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113933965..113936589-chr2:113937925..113940404,2	MCF-7	breast:
2	chr2:113914767..113917449-chr2:113937885..113940587,3	MCF-7	breast:
3	chr2:113939010..113941209-chr2:113958366..113960535,2	K562	blood:
4	chr2:113839317..113841682-chr2:113938699..113940328,2	K562	blood:

No data

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17043069	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45627232	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55746251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7570503	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised 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	14 gene(s)	inside rSNPs	diseases
4	nsv874897	chr2:113935407-113944762	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113923000-113956000	Weak transcription	HMEC	breast
3	chr2:113934200-113949000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:113934400-113948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113934600-113940800	Genic enhancers	Fetal Thymus	thymus
7	chr2:113934600-113941000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:113934600-113946400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:113935200-113942800	Genic enhancers	Dnd41	blood
10	chr2:113936800-113940400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:113937800-113940400	Enhancers	Pancreas	Pancrea
12	chr2:113938000-113945000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:113938800-113945800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:113939000-113944200	Genic enhancers	Spleen	Spleen
15	chr2:113939000-113944600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:113939200-113941000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:113939200-113945600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:113939400-113940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:113939400-113941000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:113939400-113941000	Strong transcription	Fetal Intestine Small	intestine
21	chr2:113939400-113941400	Weak transcription	NHEK	skin
22	chr2:113939400-113945200	Strong transcription	Fetal Stomach	stomach
23	chr2:113939400-113945400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:113939400-113946400	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr2:113939400-113946800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:113939400-113948400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:113939400-113949000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
30	chr2:113939600-113941000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:113939600-113941000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:113939600-113941600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:113939600-113941600	Genic enhancers	Placenta	Placenta
34	chr2:113939600-113942200	Strong transcription	GM12878-XiMat	blood
35	chr2:113939600-113943000	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr2:113939600-113943200	Weak transcription	Adipose Nuclei	Adipose
37	chr2:113939600-113943200	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:113939600-113945600	Strong transcription	K562	blood
39	chr2:113939600-113947800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr2:113939600-113953800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:113939600-113955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:113939600-113956200	Weak transcription	Fetal Lung	lung
43	chr2:113939800-113940600	Genic enhancers	Primary T cells from cord blood	blood
44	chr2:113939800-113940600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:113939800-113940800	Weak transcription	Fetal Intestine Large	intestine
46	chr2:113939800-113941000	Strong transcription	Primary B cells from cord blood	blood
47	chr2:113939800-113941200	Weak transcription	Stomach Mucosa	stomach
48	chr2:113939800-113941400	Strong transcription	Esophagus	oesophagus
49	chr2:113939800-113941800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:113939800-113942200	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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