Variant report

Variant	rs907482
Chromosome Location	chr12:122747023-122747024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122747009..122749656-chr12:122904733..122907639,2	K562	blood:

Variant related genes	Relation type
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10270	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846470	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11060802	0.81[EUR][1000 genomes]
rs11061609	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12423987	0.86[JPT][hapmap]
rs12424872	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs12578815	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs12578953	0.87[EUR][1000 genomes]
rs12580084	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809220	0.84[ASN][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12814923	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs12815512	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12816499	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs12820704	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs12822121	0.86[JPT][hapmap]
rs12824701	1.00[JPT][hapmap]
rs12824925	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12825149	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12825279	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs12828234	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12833379	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512023	0.90[JPT][hapmap]
rs2063510	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2068223	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs2271408	0.83[CEU][hapmap]
rs2271409	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs2277332	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34325222	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782153	0.88[ASN][1000 genomes]
rs3782154	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809116	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs4567503	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758649	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs4758650	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758670	0.87[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758671	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55741463	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59734396	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488876	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298397	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7388	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7957569	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963144	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963565	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7964911	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7965868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7970027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972228	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs872451	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs907483	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9668064	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs907482	VPS33A	cis	lymphoblastoid	seeQTL
rs907482	IL31	cis	parietal	SCAN
rs907482	GPR109A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122711800-122749600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122711800-122749600	Weak transcription	Psoas Muscle	Psoas
3	chr12:122712400-122748600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:122713800-122748800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:122716000-122749600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:122716000-122750200	Weak transcription	Fetal Kidney	kidney
7	chr12:122717200-122750000	Weak transcription	Fetal Heart	heart
8	chr12:122720600-122750000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122720600-122750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:122721600-122750400	Weak transcription	Small Intestine	intestine
11	chr12:122722000-122750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:122730600-122749600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:122730800-122748800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:122731200-122748200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:122731400-122748600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:122731800-122748200	Strong transcription	Fetal Intestine Large	intestine
17	chr12:122731800-122748600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:122731800-122748800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:122732200-122748200	Strong transcription	Fetal Stomach	stomach
20	chr12:122732400-122748200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:122732600-122747800	Strong transcription	Thymus	Thymus
22	chr12:122732800-122748600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:122733400-122749600	Weak transcription	Colonic Mucosa	Colon
24	chr12:122733400-122750000	Weak transcription	HSMMtube	muscle
25	chr12:122733600-122749600	Weak transcription	HMEC	breast
26	chr12:122734200-122749600	Weak transcription	HepG2	liver
27	chr12:122735200-122748400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:122735400-122749000	Weak transcription	Fetal Brain Male	brain
29	chr12:122735400-122749600	Weak transcription	Stomach Mucosa	stomach
30	chr12:122735400-122750000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:122735800-122747200	Weak transcription	NHLF	lung
32	chr12:122737000-122747400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:122737000-122748600	Strong transcription	Primary T cells from cord blood	blood
34	chr12:122737000-122748600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:122737000-122748600	Strong transcription	Fetal Thymus	thymus
36	chr12:122737000-122748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:122737200-122748800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:122737200-122748800	Strong transcription	Liver	Liver
39	chr12:122737400-122748200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:122737600-122749600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:122738400-122748200	Strong transcription	Fetal Muscle Leg	muscle
42	chr12:122738400-122748800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:122738600-122749200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:122738800-122748200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:122739000-122748400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:122739200-122748200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:122739400-122749000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:122739600-122748200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:122739800-122747200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:122740000-122747600	Strong transcription	Spleen	Spleen

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