Variant report

Variant	rs2239860
Chromosome Location	chr12:51414754-51414755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:51404293..51409685-chr12:51411834..51415817,7	K562	blood:
2	chr12:51399342..51401047-chr12:51411160..51415071,3	MCF-7	breast:
3	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
4	chr12:51400476..51402543-chr12:51413177..51415627,2	K562	blood:
5	chr12:51381778..51384453-chr12:51414411..51415934,2	MCF-7	breast:
6	chr12:51155647..51158511-chr12:51413575..51415809,2	K562	blood:
7	chr12:51393084..51395626-chr12:51414543..51417529,2	MCF-7	breast:
8	chr12:51386892..51388716-chr12:51412820..51415080,2	K562	blood:
9	chr12:51412418..51415100-chr12:51610730..51614429,3	K562	blood:
10	chr12:51413146..51415760-chr12:51440931..51443529,2	MCF-7	breast:
11	chr12:51403352..51405981-chr12:51411330..51414858,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272028	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10876122	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169625	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169629	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169634	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169640	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169643	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169651	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169653	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169658	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169662	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169674	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169675	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169681	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12227734	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982777	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016533	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2269682	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809320	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768871	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7295893	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS 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	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
3	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
6	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
7	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
9	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:51403600-51417600	Weak transcription	HSMM	muscle
15	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
16	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
17	chr12:51405800-51415000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:51406000-51415200	Weak transcription	Right Atrium	heart
19	chr12:51406400-51417200	Weak transcription	Fetal Brain Male	brain
20	chr12:51406400-51417400	Weak transcription	Osteobl	bone
21	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:51406800-51415000	Weak transcription	Fetal Heart	heart
23	chr12:51407000-51414800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:51407200-51415800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:51407400-51415200	Weak transcription	Placenta	Placenta
29	chr12:51407600-51415200	Weak transcription	Lung	lung
30	chr12:51407600-51415600	Weak transcription	Small Intestine	intestine
31	chr12:51407600-51417200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:51407600-51417600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:51408600-51417000	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:51408600-51417000	Weak transcription	Psoas Muscle	Psoas
35	chr12:51409000-51417400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:51409800-51416400	Weak transcription	Fetal Kidney	kidney
37	chr12:51410400-51415200	Weak transcription	Pancreas	Pancrea
38	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
39	chr12:51411800-51415600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:51411800-51416400	Weak transcription	A549	lung
41	chr12:51412200-51417800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:51412400-51414800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:51412400-51415600	Enhancers	Brain Hippocampus Middle	brain
44	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:51412800-51414800	Enhancers	Dnd41	blood
46	chr12:51412800-51415400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:51412800-51415400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:51412800-51416200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr12:51412800-51416600	Enhancers	Brain Substantia Nigra	brain
50	chr12:51412800-51417800	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links