Variant report

Variant	rs2463442
Chromosome Location	chr12:105144974-105144975
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1002803	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10507184	0.84[CEU][hapmap]
rs1070316	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1155994	0.84[CEU][hapmap]
rs1389610	0.80[EUR][1000 genomes]
rs1389612	0.84[CEU][hapmap]
rs1474459	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2131806	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248012	0.84[CEU][hapmap]
rs2453154	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2453155	0.89[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2453156	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2453161	0.94[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2453166	0.84[CEU][hapmap]
rs2463018	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463019	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463437	0.89[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2463438	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2463439	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2463440	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2463441	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2463443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2468089	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs2468099	0.84[CEU][hapmap]
rs2468105	0.84[CEU][hapmap]
rs2468109	0.94[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2468110	0.94[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2468112	0.82[EUR][1000 genomes]
rs2642109	0.82[EUR][1000 genomes]
rs2730291	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6539170	0.84[CEU][hapmap]
rs703681	0.94[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7847	0.82[EUR][1000 genomes]
rs903247	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2463442	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105130000-105150800	Weak transcription	A549	lung
2	chr12:105130200-105150200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:105133800-105151200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:105136600-105150600	Weak transcription	Gastric	stomach
5	chr12:105136800-105154400	Weak transcription	Right Ventricle	heart
6	chr12:105137000-105150800	Weak transcription	Aorta	Aorta
7	chr12:105137000-105152600	Weak transcription	Brain Angular Gyrus	brain
8	chr12:105137200-105150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:105137200-105150600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:105137200-105154000	Weak transcription	Brain Substantia Nigra	brain
11	chr12:105137200-105157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:105139000-105147000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:105139600-105147200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:105139800-105146000	Enhancers	Fetal Thymus	thymus
15	chr12:105140000-105145200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:105140200-105145000	Enhancers	Placenta	Placenta
17	chr12:105140200-105146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:105141000-105145800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:105141000-105146200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:105141200-105145800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:105141600-105145000	Enhancers	Dnd41	blood
22	chr12:105141600-105155400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:105142400-105150600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:105142400-105150800	Weak transcription	Brain Germinal Matrix	brain
25	chr12:105142400-105154600	Weak transcription	Fetal Brain Male	brain
26	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:105142600-105146200	Enhancers	Thymus	Thymus
28	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:105142800-105149000	Weak transcription	Right Atrium	heart
30	chr12:105142800-105149800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:105142800-105150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:105142800-105150600	Weak transcription	Fetal Stomach	stomach
33	chr12:105142800-105150800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:105142800-105154800	Weak transcription	Fetal Brain Female	brain
35	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:105143000-105145000	Weak transcription	Psoas Muscle	Psoas
37	chr12:105143000-105146200	Enhancers	Primary B cells from cord blood	blood
38	chr12:105143000-105146800	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:105143000-105150600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:105143000-105150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:105143200-105150000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:105143200-105150000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:105143400-105145200	Enhancers	Adipose Nuclei	Adipose
44	chr12:105143400-105146000	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:105143600-105145800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:105143600-105150600	Weak transcription	Lung	lung
47	chr12:105143600-105151000	Weak transcription	HSMMtube	muscle
48	chr12:105143600-105154200	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:105143800-105145600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr12:105143800-105156800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links