Variant report

Variant	rs61538288
Chromosome Location	chr2:187354404-187354405
allele	C/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	TBL1XR1	chr2:187354025-187354670	K562	blood:	n/a	n/a
2	POLR2A	chr2:187353036-187357373	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187352160..187354477-chr2:187361786..187364849,3	MCF-7	breast:
2	chr2:187352868..187356509-chr2:187367066..187369424,5	K562	blood:

Variant related genes	Relation type
DPRXP1	TF binding region
ENSG00000213953	Chromatin interaction
ENSG00000268846	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10931241	0.93[EUR][1000 genomes]
rs12622084	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1376781	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1597244	0.93[EUR][1000 genomes]
rs16827790	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16827800	0.93[EUR][1000 genomes]
rs3754582	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144823	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4606885	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59228985	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72895425	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72895447	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72895498	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72897378	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561955	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9636305	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187351800-187355200	Weak transcription	Esophagus	oesophagus
2	chr2:187351800-187361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:187351800-187362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:187352000-187355000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:187352000-187357800	Weak transcription	Pancreas	Pancrea
6	chr2:187352200-187355200	Weak transcription	Left Ventricle	heart
7	chr2:187352200-187365400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:187352200-187365400	Weak transcription	Lung	lung
9	chr2:187352400-187355600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr2:187352400-187358000	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:187352400-187358200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:187352400-187358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:187352400-187358400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:187352400-187358600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:187352400-187358800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:187352400-187358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:187352400-187358800	Enhancers	Colon Smooth Muscle	Colon
18	chr2:187352400-187358800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:187352400-187359000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:187352400-187359400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:187352400-187360000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:187352400-187360000	Weak transcription	Placenta	Placenta
23	chr2:187352600-187355200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:187352600-187357000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:187352600-187357000	Weak transcription	Fetal Thymus	thymus
26	chr2:187352600-187357200	Enhancers	Liver	Liver
27	chr2:187352600-187358000	Enhancers	Brain Angular Gyrus	brain
28	chr2:187352600-187358600	Enhancers	Brain Anterior Caudate	brain
29	chr2:187352600-187359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:187352600-187360200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:187352600-187360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:187352600-187360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:187352600-187362600	Weak transcription	HSMMtube	muscle
34	chr2:187352800-187355600	Enhancers	Ovary	ovary
35	chr2:187352800-187356000	Enhancers	Fetal Intestine Small	intestine
36	chr2:187353000-187357200	Enhancers	Small Intestine	intestine
37	chr2:187353200-187356000	Weak transcription	Fetal Brain Female	brain
38	chr2:187353200-187357800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:187353200-187360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:187353400-187354600	Transcr. at gene 5' and 3'	K562	blood
41	chr2:187353400-187358200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:187353400-187360000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:187353400-187361800	Weak transcription	Fetal Heart	heart
44	chr2:187353600-187355200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:187353600-187355200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:187353600-187355400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:187353600-187355400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:187353600-187355600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:187353600-187356000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:187353600-187357600	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links