Variant report

Variant	rs12903283
Chromosome Location	chr15:56921147-56921148
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	chr15:56917635..56921427-chr15:56927858..56931559,3	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10152127	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518870	0.86[MEX][hapmap]
rs11071280	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630168	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs11633363	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11635333	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636994	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638580	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11638707	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11852277	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857388	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148500	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442189	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591502	0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592389	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595822	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12898521	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12898760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12900244	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12901887	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12903336	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12905514	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12906830	0.84[EUR][1000 genomes]
rs12908906	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910442	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910459	0.81[CEU][hapmap]
rs12911191	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12911381	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912666	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs12913361	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12916079	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1424694	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs16977020	0.90[CHB][hapmap]
rs17238845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994081	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170459	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170463	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279298	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2279299	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs2414480	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28480089	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28620278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784554	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816752	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs3929265	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774244	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4774884	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774886	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521904	0.81[EUR][1000 genomes]
rs538382	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs553421	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs7162317	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7168178	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs7174432	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178796	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182187	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs795032	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8025391	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8036217	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8041540	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8043223	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.91[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12903283	TCF12	cis	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56902800-56945400	Weak transcription	Right Ventricle	heart
2	chr15:56905600-56923600	Weak transcription	Left Ventricle	heart
3	chr15:56908800-56923400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:56910600-56945400	Weak transcription	HSMMtube	muscle
5	chr15:56912800-56923400	Weak transcription	Adipose Nuclei	Adipose
6	chr15:56912800-56923400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr15:56912800-56957000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:56913000-56923400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:56913200-56923200	Weak transcription	HSMM	muscle
10	chr15:56913200-56923600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:56913200-56929600	Weak transcription	NHDF-Ad	bronchial
12	chr15:56913400-56923600	Weak transcription	Dnd41	blood
13	chr15:56913400-56955200	Weak transcription	Aorta	Aorta
14	chr15:56914000-56929400	Weak transcription	Fetal Stomach	stomach
15	chr15:56914200-56921200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:56915200-56937400	Weak transcription	Liver	Liver
17	chr15:56915400-56923600	Weak transcription	Primary T cells from cord blood	blood
18	chr15:56915600-56929000	Weak transcription	Thymus	Thymus
19	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
20	chr15:56916800-56949800	Weak transcription	Fetal Kidney	kidney
21	chr15:56917200-56955200	Weak transcription	Psoas Muscle	Psoas
22	chr15:56917600-56921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:56917600-56923600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:56917600-56944800	Weak transcription	Fetal Brain Male	brain
25	chr15:56917600-56957000	Weak transcription	Brain Anterior Caudate	brain
26	chr15:56917800-56923200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:56917800-56923200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:56917800-56923400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:56917800-56923400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:56917800-56923400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:56917800-56923600	Weak transcription	Primary B cells from cord blood	blood
32	chr15:56917800-56938200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:56917800-56945400	Weak transcription	GM12878-XiMat	blood
34	chr15:56917800-56955800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:56917800-56956800	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
37	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:56917800-56990600	Weak transcription	NHLF	lung
39	chr15:56918000-56921200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:56918000-56923600	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:56918000-56923600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:56918000-56923600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:56918000-56923600	Weak transcription	Fetal Lung	lung
44	chr15:56918000-56923600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:56918000-56945200	Weak transcription	A549	lung
46	chr15:56918000-56945600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:56918200-56923600	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:56918200-56925200	Strong transcription	Fetal Thymus	thymus
49	chr15:56918400-56945400	Weak transcription	Fetal Intestine Small	intestine
50	chr15:56918400-56957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links