Variant report

Variant	rs2463019
Chromosome Location	chr12:105144536-105144537
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	chr12:105130507..105133001-chr12:105142038..105144910,2	MCF-7	breast:
2	chr12:105143178..105144932-chr12:105145458..105148158,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1002803	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1070316	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1389610	0.80[EUR][1000 genomes]
rs1474459	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131806	0.82[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453154	0.83[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2453155	0.83[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2453156	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2453161	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2463018	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463437	0.83[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2463438	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2463439	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs2463440	0.83[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2463441	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2463442	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]
rs2463443	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463444	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468109	0.89[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2468110	0.89[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[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	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs703681	0.89[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7847	0.82[EUR][1000 genomes]
rs903247	0.83[CEU][hapmap];0.87[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
rs2463019	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 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	chr12:105136600-105144800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:105136600-105150600	Weak transcription	Gastric	stomach
6	chr12:105136800-105154400	Weak transcription	Right Ventricle	heart
7	chr12:105137000-105150800	Weak transcription	Aorta	Aorta
8	chr12:105137000-105152600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:105137200-105144800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:105137200-105150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:105137200-105150600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:105137200-105154000	Weak transcription	Brain Substantia Nigra	brain
13	chr12:105137200-105157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:105139000-105144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:105139000-105147000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:105139600-105147200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:105139800-105144600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:105139800-105146000	Enhancers	Fetal Thymus	thymus
19	chr12:105140000-105145200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:105140200-105145000	Enhancers	Placenta	Placenta
21	chr12:105140200-105146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:105141000-105145800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:105141000-105146200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr12:105141200-105145800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:105141600-105145000	Enhancers	Dnd41	blood
26	chr12:105141600-105155400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:105142400-105144800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:105142400-105150600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:105142400-105150800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:105142400-105154600	Weak transcription	Fetal Brain Male	brain
31	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:105142600-105144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:105142600-105144800	Weak transcription	Brain Anterior Caudate	brain
34	chr12:105142600-105144800	Weak transcription	Spleen	Spleen
35	chr12:105142600-105144800	Enhancers	GM12878-XiMat	blood
36	chr12:105142600-105146200	Enhancers	Thymus	Thymus
37	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:105142800-105144800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:105142800-105144800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:105142800-105149000	Weak transcription	Right Atrium	heart
41	chr12:105142800-105149800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:105142800-105150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:105142800-105150600	Weak transcription	Fetal Stomach	stomach
44	chr12:105142800-105150800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:105142800-105154800	Weak transcription	Fetal Brain Female	brain
46	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:105143000-105144600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:105143000-105144800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:105143000-105144800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:105143000-105145000	Weak transcription	Psoas Muscle	Psoas

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