Variant report

Variant	rs13405727
Chromosome Location	chr2:182779184-182779185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:182779161-182779323	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:182778854-182784341	HCT-116	colon:	n/a	n/a
3	POLR2A	chr2:182779182-182784349	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:182774475..182776791-chr2:182778297..182781131,4	MCF-7	breast:
2	chr2:182775981..182777608-chr2:182777647..182779406,3	K562	blood:
3	chr2:182777511..182779928-chr2:182940504..182943969,3	MCF-7	breast:
4	chr2:182775265..182779288-chr2:182885219..182887763,3	MCF-7	breast:
5	chr2:182778913..182780583-chr2:182786458..182788567,2	K562	blood:

No data

Variant related genes	Relation type
SSFA2	TF binding region
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10171957	0.82[YRI][hapmap]
rs10181991	1.00[AMR][1000 genomes]
rs11887558	1.00[AMR][1000 genomes]
rs11890230	1.00[AMR][1000 genomes]
rs11894897	1.00[AMR][1000 genomes]
rs11896011	1.00[AMR][1000 genomes]
rs11898245	1.00[AMR][1000 genomes]
rs11903559	1.00[AMR][1000 genomes]
rs13384392	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13384479	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13395789	1.00[AMR][1000 genomes]
rs13407143	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419020	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16867501	1.00[AMR][1000 genomes]
rs73032631	1.00[AMR][1000 genomes]
rs73032655	1.00[AMR][1000 genomes]
rs73032661	1.00[AMR][1000 genomes]
rs73032669	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73032673	1.00[AMR][1000 genomes]
rs73032699	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73038912	1.00[AMR][1000 genomes]
rs73038938	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182757800-182779400	Weak transcription	Esophagus	oesophagus
2	chr2:182757800-182779800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:182757800-182790400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:182758000-182780000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:182758000-182783200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:182758200-182779800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:182758200-182780200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:182759200-182783800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:182759600-182779600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:182759600-182782000	Strong transcription	HSMM	muscle
11	chr2:182759800-182789400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:182760000-182794800	Strong transcription	Fetal Thymus	thymus
13	chr2:182760800-182787000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:182761400-182779400	Weak transcription	Fetal Stomach	stomach
15	chr2:182761400-182795800	Strong transcription	Placenta	Placenta
16	chr2:182762000-182779400	Weak transcription	Aorta	Aorta
17	chr2:182762000-182780000	Weak transcription	Fetal Heart	heart
18	chr2:182764600-182786600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:182765200-182779200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:182765200-182779400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:182765200-182779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:182765200-182780400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:182765400-182779200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:182767000-182779800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:182767200-182783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:182767600-182780000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:182767800-182779400	Weak transcription	Gastric	stomach
28	chr2:182768000-182779400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:182768000-182779600	Weak transcription	Ovary	ovary
30	chr2:182768000-182780000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:182768200-182779600	Weak transcription	Lung	lung
32	chr2:182768200-182779600	Weak transcription	Psoas Muscle	Psoas
33	chr2:182768200-182787800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:182768400-182779200	Weak transcription	Primary B cells from cord blood	blood
35	chr2:182768400-182779800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:182769400-182795600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:182769600-182779400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:182769600-182795800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:182769600-182795800	Strong transcription	Dnd41	blood
40	chr2:182771600-182779400	Weak transcription	Left Ventricle	heart
41	chr2:182771600-182779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:182772000-182779400	Weak transcription	Right Ventricle	heart
43	chr2:182772400-182790800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:182773600-182780800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr2:182774000-182780600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:182774000-182781400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:182774000-182790800	Strong transcription	HMEC	breast
48	chr2:182774200-182780600	Strong transcription	NHLF	lung
49	chr2:182774200-182780800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:182774200-182781000	Strong transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links