Variant report

Variant	rs2271408
Chromosome Location	chr12:122720310-122720311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122688392..122691286-chr12:122720217..122723089,2	K562	blood:
2	chr12:122718778..122721345-chr12:122749613..122752593,4	K562	blood:
3	chr12:122710865..122714280-chr12:122719440..122723902,5	K562	blood:
4	chr12:122718153..122722720-chr12:122747051..122751467,5	MCF-7	breast:
5	chr12:122715428..122718319-chr12:122718788..122721309,2	MCF-7	breast:
6	chr12:122710328..122713101-chr12:122719440..122721142,3	K562	blood:

Variant related genes	Relation type
ENSG00000176383	Chromatin interaction
ENSG00000139719	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000184047	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10270	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10848035	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11060333	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12423987	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12424872	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12425684	0.81[EUR][1000 genomes]
rs12578739	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12578863	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580084	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs12809220	0.85[EUR][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.85[EUR][1000 genomes]
rs12814516	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12814923	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs12816400	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12816499	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12820704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12822121	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs12824385	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap]
rs12824925	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs12825008	0.86[EUR][1000 genomes]
rs12825149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs12825279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12826834	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12827843	0.87[EUR][1000 genomes]
rs12831210	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1512023	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs1967291	0.87[EUR][1000 genomes]
rs2068223	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2277333	0.86[EUR][1000 genomes]
rs34383196	0.84[EUR][1000 genomes]
rs35030971	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35772530	0.88[EUR][1000 genomes]
rs35963777	0.81[EUR][1000 genomes]
rs3809116	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4758650	0.83[CEU][hapmap]
rs4758677	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6488906	0.83[EUR][1000 genomes]
rs6488909	0.82[EUR][1000 genomes]
rs7388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs7962385	0.83[CEU][hapmap]
rs7963565	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs7970027	0.83[CEU][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2271408	VPS33A	cis	multi-tissue	Pritchard
rs2271408	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122711400-122734200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:122711600-122721800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:122711800-122734400	Weak transcription	Stomach Mucosa	stomach
4	chr12:122711800-122734800	Weak transcription	Fetal Brain Male	brain
5	chr12:122711800-122749600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:122711800-122749600	Weak transcription	Psoas Muscle	Psoas
7	chr12:122712000-122730000	Strong transcription	Fetal Intestine Large	intestine
8	chr12:122712200-122722000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:122712200-122730800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:122712400-122720600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:122712400-122748600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:122713400-122722000	Strong transcription	Left Ventricle	heart
13	chr12:122713600-122720600	Strong transcription	Primary B cells from cord blood	blood
14	chr12:122713600-122722000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr12:122713600-122725000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:122713600-122726800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:122713800-122722000	Strong transcription	Placenta	Placenta
18	chr12:122713800-122722200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:122713800-122726800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:122713800-122727800	Strong transcription	Fetal Thymus	thymus
21	chr12:122713800-122729400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:122713800-122730800	Strong transcription	Adipose Nuclei	Adipose
23	chr12:122713800-122731000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:122713800-122731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:122713800-122748800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr12:122714000-122720600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:122714000-122722000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:122714000-122723800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:122714000-122727000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:122714000-122727000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:122714000-122727200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:122714000-122729600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:122714200-122720600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:122714200-122721400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:122714200-122729800	Strong transcription	Fetal Intestine Small	intestine
36	chr12:122714400-122722200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:122714400-122725000	Strong transcription	Fetal Brain Female	brain
38	chr12:122714400-122726800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:122714400-122729000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:122714400-122729400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:122714400-122729400	Strong transcription	Fetal Stomach	stomach
42	chr12:122714400-122729600	Strong transcription	Thymus	Thymus
43	chr12:122714600-122723400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:122714600-122729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:122715000-122720600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:122715000-122720600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:122715000-122721400	Strong transcription	Right Ventricle	heart
48	chr12:122715000-122721600	Strong transcription	Brain Angular Gyrus	brain
49	chr12:122715000-122722000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:122715000-122722000	Strong transcription	Brain Substantia Nigra	brain

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