Variant report

Variant	rs2141248
Chromosome Location	chr12:105159761-105159762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1002803	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs1038968	0.85[EUR][1000 genomes]
rs10507184	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1070316	0.81[JPT][hapmap]
rs10746008	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10778358	0.81[JPT][hapmap]
rs1155994	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316594	0.91[EUR][1000 genomes]
rs1389609	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1389612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474459	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1565813	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1565815	0.91[EUR][1000 genomes]
rs2047124	0.84[EUR][1000 genomes]
rs2131806	0.86[CEU][hapmap]
rs2245927	0.91[EUR][1000 genomes]
rs2245931	0.91[EUR][1000 genomes]
rs2248012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249454	0.81[JPT][hapmap]
rs2453154	0.93[CEU][hapmap]
rs2453155	0.93[CEU][hapmap]
rs2453156	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453157	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453158	0.87[EUR][1000 genomes]
rs2453160	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453161	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2453166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2453167	0.91[EUR][1000 genomes]
rs2453168	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2463016	0.91[EUR][1000 genomes]
rs2463017	0.91[EUR][1000 genomes]
rs2463018	0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2463025	0.91[EUR][1000 genomes]
rs2463429	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2463431	0.84[EUR][1000 genomes]
rs2463432	0.90[EUR][1000 genomes]
rs2463433	0.91[EUR][1000 genomes]
rs2463437	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2463438	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463439	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2463440	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2463441	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2463442	0.80[CEU][hapmap]
rs2463443	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2463444	0.81[CEU][hapmap]
rs2468083	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2468089	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2468090	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2468092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468099	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468100	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468109	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2468110	0.86[CEU][hapmap]
rs2468340	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2565167	0.91[EUR][1000 genomes]
rs2642110	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2642116	0.91[EUR][1000 genomes]
rs2730291	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730295	0.85[EUR][1000 genomes]
rs2731030	0.85[EUR][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs4393404	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs6539167	0.84[EUR][1000 genomes]
rs6539170	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6539171	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs703681	0.86[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs7135015	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7847	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7968763	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7980681	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903247	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv899496	chr12:105152391-105199038	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2141248	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105143800-105160800	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:105145400-105161200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:105145600-105162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:105145800-105161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:105145800-105161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:105145800-105161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:105146000-105161400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:105146800-105161200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:105151400-105161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:105151600-105160800	Weak transcription	Esophagus	oesophagus
12	chr12:105151600-105161800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:105151600-105162800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:105152400-105162600	Weak transcription	Brain Anterior Caudate	brain
15	chr12:105153200-105161800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:105154400-105162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:105156200-105160800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:105156200-105160800	Weak transcription	Brain Germinal Matrix	brain
19	chr12:105156200-105163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:105156400-105161400	Weak transcription	Fetal Brain Male	brain
21	chr12:105157000-105159800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:105157200-105161000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:105157400-105162600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:105157400-105162600	Weak transcription	NHEK	skin
25	chr12:105157400-105162800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:105157600-105162000	Weak transcription	HMEC	breast
27	chr12:105157600-105162200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:105157800-105159800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:105158400-105159800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr12:105158800-105161000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:105158800-105161800	Weak transcription	Ovary	ovary
32	chr12:105159200-105159800	Enhancers	Primary neutrophils fromperipheralblood	blood

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