Variant report

Variant	rs2271409
Chromosome Location	chr12:122762604-122762605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122750460..122753402-chr12:122760156..122762778,3	K562	blood:
2	chr12:122709020..122710648-chr12:122761773..122763622,2	MCF-7	breast:
3	chr12:122748134..122753515-chr12:122760156..122766963,8	K562	blood:

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

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10270	0.83[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10848035	0.83[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap]
rs11060333	0.95[CEU][hapmap]
rs12423987	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424872	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12425684	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578739	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12578815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes]
rs12578863	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12578953	0.92[ASN][1000 genomes]
rs12580084	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12809220	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12814516	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12814554	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12814923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12815053	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12816400	0.84[EUR][1000 genomes]
rs12816499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12820704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12822121	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824385	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes]
rs12824925	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12825008	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12825279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826834	0.86[EUR][1000 genomes]
rs12828234	0.81[ASN][1000 genomes]
rs12831210	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512023	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1967291	0.84[EUR][1000 genomes]
rs2063510	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs2068223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2277332	0.86[JPT][hapmap]
rs2277333	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34383196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35030971	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35772530	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35963777	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782153	0.88[EUR][1000 genomes]
rs3782154	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3809116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4567503	0.86[JPT][hapmap]
rs4758649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758650	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs4758670	0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4758677	0.95[CEU][hapmap]
rs56219573	0.82[AFR][1000 genomes]
rs60317410	0.82[AFR][1000 genomes]
rs6488906	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488909	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71082959	0.82[AFR][1000 genomes]
rs7388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7962385	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7963565	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs7970027	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7972227	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap];0.86[JPT][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2271409	GPR109A	cis	cerebellum	SCAN
rs2271409	IL31	cis	parietal	SCAN
rs2271409	MLXIP	Cis_1M	lymphoblastoid	RTeQTL
rs2271409	DIABLO	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122751600-122803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:122751800-122762800	Weak transcription	Psoas Muscle	Psoas
3	chr12:122751800-122762800	Weak transcription	Small Intestine	intestine
4	chr12:122752000-122762800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:122752000-122762800	Weak transcription	K562	blood
6	chr12:122752000-122763000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:122752000-122764000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:122752000-122764000	Weak transcription	Fetal Heart	heart
9	chr12:122752000-122764200	Weak transcription	Stomach Mucosa	stomach
10	chr12:122752000-122766400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:122752000-122780000	Weak transcription	Fetal Kidney	kidney
12	chr12:122752000-122800600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:122752000-122802600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:122752200-122766800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:122752400-122762800	Weak transcription	Fetal Brain Male	brain
16	chr12:122752400-122810400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:122752600-122765200	Weak transcription	Hela-S3	cervix
18	chr12:122754600-122822400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:122755200-122764000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:122755400-122764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:122755400-122765800	Strong transcription	Adipose Nuclei	Adipose
22	chr12:122755800-122768200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:122756000-122766200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:122756200-122766800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:122756600-122766000	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:122757000-122763600	Strong transcription	Fetal Intestine Small	intestine
27	chr12:122757200-122763000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:122757200-122766200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:122757600-122762800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:122757600-122780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:122757800-122762800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:122757800-122762800	Weak transcription	HUVEC	blood vessel
33	chr12:122758200-122762800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:122758200-122762800	Weak transcription	Fetal Brain Female	brain
35	chr12:122758200-122764000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:122758600-122762800	Weak transcription	Colonic Mucosa	Colon
37	chr12:122758600-122762800	Weak transcription	Gastric	stomach
38	chr12:122758600-122763000	Weak transcription	Ovary	ovary
39	chr12:122758800-122762800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:122758800-122762800	Weak transcription	Brain Angular Gyrus	brain
41	chr12:122758800-122762800	Weak transcription	Thymus	Thymus
42	chr12:122758800-122763000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:122758800-122764400	Weak transcription	NH-A	brain
44	chr12:122759000-122762800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:122759000-122762800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:122759000-122762800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:122759000-122762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:122759000-122762800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:122759000-122762800	Weak transcription	Spleen	Spleen
50	chr12:122759000-122763000	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links