Variant report

Variant	rs2463429
Chromosome Location	chr12:105178441-105178442
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	chr12:105173249..105175093-chr12:105175948..105178622,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1038968	0.89[EUR][1000 genomes]
rs10507184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1070316	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs10746008	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10778358	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1155994	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316594	0.96[EUR][1000 genomes]
rs1389609	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474459	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1565813	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1565815	0.96[EUR][1000 genomes]
rs2047124	0.89[EUR][1000 genomes]
rs2088019	0.80[EUR][1000 genomes]
rs2131806	0.88[CEU][hapmap]
rs2141248	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245927	0.96[EUR][1000 genomes]
rs2245929	0.81[EUR][1000 genomes]
rs2245931	0.96[EUR][1000 genomes]
rs2248012	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249454	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2453154	0.94[CEU][hapmap]
rs2453155	0.94[CEU][hapmap]
rs2453156	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453157	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453158	0.93[EUR][1000 genomes]
rs2453160	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453161	0.88[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2453166	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453167	0.96[EUR][1000 genomes]
rs2453168	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463016	0.96[EUR][1000 genomes]
rs2463017	0.96[EUR][1000 genomes]
rs2463018	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2463020	0.81[EUR][1000 genomes]
rs2463025	0.96[EUR][1000 genomes]
rs2463431	0.89[EUR][1000 genomes]
rs2463432	0.96[EUR][1000 genomes]
rs2463433	0.96[EUR][1000 genomes]
rs2463434	0.81[EUR][1000 genomes]
rs2463435	0.80[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2463441	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs2463442	0.83[CEU][hapmap]
rs2463443	0.84[CEU][hapmap]
rs2463444	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2468082	0.81[EUR][1000 genomes]
rs2468083	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468089	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2468090	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2468092	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468099	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468100	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468109	0.88[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2468110	0.88[CEU][hapmap]
rs2468112	0.84[EUR][1000 genomes]
rs2468340	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2565167	0.96[EUR][1000 genomes]
rs2642110	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642116	0.96[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730295	0.90[EUR][1000 genomes]
rs2731030	0.90[EUR][1000 genomes]
rs4388976	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs4393404	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6539167	0.89[EUR][1000 genomes]
rs6539170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6539171	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs703681	0.88[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs7135015	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7847	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968763	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7980681	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs903247	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2463429	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105174600-105182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:105178000-105186400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:105178200-105178800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:105178200-105179000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:105178200-105179000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105178200-105179200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:105178400-105178800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:105178400-105178800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:105178400-105178800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:105178400-105178800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr12:105178400-105178800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:105178400-105178800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:105178400-105178800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:105178400-105178800	Enhancers	Fetal Muscle Leg	muscle
15	chr12:105178400-105179000	Enhancers	Fetal Heart	heart
16	chr12:105178400-105179000	Enhancers	Fetal Stomach	stomach
17	chr12:105178400-105179200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:105178400-105179600	Enhancers	Ovary	ovary

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