Variant report

Variant	rs45550936
Chromosome Location	chr2:113934221-113934222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:113934218-113934759	MCF-7	breast:	n/a	chr2:113934239-113934249
2	POLR2A	chr2:113930967-113935020	GM12878	blood:	n/a	n/a
3	RAD21	chr2:113934208-113934709	MCF-7	breast:	n/a	chr2:113934602-113934612 chr2:113934600-113934612
4	POLR2A	chr2:113930698-113934407	GM12878	blood:	n/a	n/a
5	WRNIP1	chr2:113932120-113934523	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:113930686-113935532	GM12891	blood:	n/a	n/a
7	MAZ	chr2:113934207-113934259	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:113931045-113935205	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:113933422-113934997	GM12892	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113916276..113917249-chr2:113934015..113934953,5	MCF-7	breast:
2	chr2:113916336..113917249-chr2:113934015..113934941,3	MCF-7	breast:
3	chr2:113920491..113922506-chr2:113933722..113935359,2	MCF-7	breast:
4	chr2:113836933..113837467-chr2:113934054..113934934,2	MCF-7	breast:
5	chr2:113933537..113935192-chr2:113956517..113958039,2	MCF-7	breast:
6	chr2:113914021..113918016-chr2:113931911..113937619,8	MCF-7	breast:
7	chr2:113913340..113916449-chr2:113931202..113934969,5	MCF-7	breast:
8	chr2:113916765..113917269-chr2:113934049..113934628,2	MCF-7	breast:
9	chr2:113895312..113896612-chr2:113933996..113935124,4	MCF-7	breast:
10	chr2:113934035..113934641-chr2:121161484..121162428,2	MCF-7	breast:
11	chr2:113933965..113936589-chr2:113937925..113940404,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234174	TF binding region
ENSG00000125637	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12711763	0.98[ASN][1000 genomes]
rs13382259	0.98[ASN][1000 genomes]
rs13400502	0.98[ASN][1000 genomes]
rs13419549	0.98[ASN][1000 genomes]
rs3738908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762494	0.80[ASN][1000 genomes]
rs45560933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45603540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542123	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
2	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113923000-113956000	Weak transcription	HMEC	breast
4	chr2:113923800-113937800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:113927600-113936200	Weak transcription	NHEK	skin
6	chr2:113928000-113935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:113930200-113935200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:113930600-113934600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr2:113930800-113937800	Weak transcription	Pancreas	Pancrea
10	chr2:113931000-113934400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr2:113931000-113935000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:113931400-113936200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:113931400-113937800	Weak transcription	Fetal Intestine Large	intestine
14	chr2:113931600-113934400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:113932000-113935200	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr2:113932000-113937600	Weak transcription	Gastric	stomach
17	chr2:113932400-113934600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:113932400-113937600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:113932400-113939400	Weak transcription	Fetal Stomach	stomach
20	chr2:113932400-113939600	Enhancers	Placenta	Placenta
21	chr2:113932600-113934400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:113932800-113934800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr2:113932800-113935800	Weak transcription	Stomach Mucosa	stomach
24	chr2:113932800-113937600	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:113933000-113934600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr2:113933000-113934800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr2:113933000-113935000	Enhancers	K562	blood
28	chr2:113933000-113935600	Enhancers	Spleen	Spleen
29	chr2:113933000-113938000	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:113933000-113938800	Weak transcription	Adipose Nuclei	Adipose
31	chr2:113933200-113934800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:113933200-113935400	Bivalent Enhancer	HepG2	liver
33	chr2:113933200-113935600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr2:113933400-113934600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:113933400-113934600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:113933400-113934600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr2:113933400-113934600	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr2:113933400-113934600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:113933400-113935000	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:113933400-113937800	Weak transcription	Small Intestine	intestine
41	chr2:113933600-113934400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:113933600-113934600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
43	chr2:113933600-113934800	Strong transcription	Fetal Intestine Small	intestine
44	chr2:113933800-113934400	Weak transcription	Esophagus	oesophagus
45	chr2:113933800-113934400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:113933800-113934800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:113933800-113936800	Weak transcription	Liver	Liver
48	chr2:113934000-113934600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
49	chr2:113934000-113934600	Weak transcription	Fetal Lung	lung
50	chr2:113934000-113934600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links