Variant report

Variant	rs2463441
Chromosome Location	chr12:105145684-105145685
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	chr12:105143178..105144932-chr12:105145458..105148158,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1038968	0.83[EUR][1000 genomes]
rs10507184	0.89[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1070316	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10778358	0.83[CHD][hapmap]
rs1155994	0.89[CEU][hapmap]
rs1389612	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs1474459	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1565813	0.83[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2047124	0.82[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2248012	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2249454	0.83[CHD][hapmap]
rs2453154	0.94[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2453155	0.94[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2453156	0.94[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453157	0.81[EUR][1000 genomes]
rs2453161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453166	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2463018	0.89[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2463019	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2463431	0.82[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2463442	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2463443	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2463444	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2468089	0.89[CEU][hapmap]
rs2468092	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2468099	0.89[CEU][hapmap]
rs2468105	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs2468109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2642110	0.80[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2730295	0.82[EUR][1000 genomes]
rs2731030	0.82[EUR][1000 genomes]
rs4393404	0.86[CHD][hapmap]
rs6539167	0.82[EUR][1000 genomes]
rs6539170	0.89[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs703681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135015	0.86[CHD][hapmap]
rs7847	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903247	0.94[CEU][hapmap];0.85[TSI][hapmap];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2463441	C12orf45	cis	lymphoblastoid	seeQTL
rs2463441	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	chr12:105136600-105150600	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	chr12:105140200-105146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:105141000-105145800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:105141000-105146200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:105141200-105145800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:105141600-105155400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:105142400-105150600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:105142400-105150800	Weak transcription	Brain Germinal Matrix	brain
22	chr12:105142400-105154600	Weak transcription	Fetal Brain Male	brain
23	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:105142600-105146200	Enhancers	Thymus	Thymus
25	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:105142800-105149000	Weak transcription	Right Atrium	heart
27	chr12:105142800-105149800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:105142800-105150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:105142800-105150600	Weak transcription	Fetal Stomach	stomach
30	chr12:105142800-105150800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:105142800-105154800	Weak transcription	Fetal Brain Female	brain
32	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:105143000-105146200	Enhancers	Primary B cells from cord blood	blood
34	chr12:105143000-105146800	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:105143000-105150600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:105143000-105150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:105143200-105150000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:105143200-105150000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:105143400-105146000	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:105143600-105145800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr12:105143600-105150600	Weak transcription	Lung	lung
42	chr12:105143600-105151000	Weak transcription	HSMMtube	muscle
43	chr12:105143600-105154200	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:105143800-105156800	Weak transcription	NHLF	lung
45	chr12:105143800-105160800	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:105144000-105150000	Weak transcription	K562	blood
47	chr12:105144000-105150600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:105144000-105150800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:105144000-105151000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:105144000-105158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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