Variant report

Variant	rs2463018
Chromosome Location	chr12:105152997-105152998
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	chr12:105140750..105142550-chr12:105151278..105155246,3	MCF-7	breast:
2	chr12:105148544..105150678-chr12:105152923..105154577,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf45-3	chr12:105151948-105155783	NONHSAT030431

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1002803	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1038968	0.82[EUR][1000 genomes]
rs10507184	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap]
rs1070316	0.83[CEU][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs10746008	0.84[CHB][hapmap]
rs10778358	0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs1155994	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1316594	0.88[EUR][1000 genomes]
rs1389609	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1389612	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs1474459	0.89[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1565813	0.83[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs1565815	0.88[EUR][1000 genomes]
rs2047124	0.81[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2141248	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245927	0.88[EUR][1000 genomes]
rs2245931	0.88[EUR][1000 genomes]
rs2248012	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2249454	0.84[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap]
rs2453154	0.94[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2453155	0.94[CEU][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2453156	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453157	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453158	0.84[EUR][1000 genomes]
rs2453160	0.88[EUR][1000 genomes]
rs2453161	0.89[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2453166	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2453167	0.88[EUR][1000 genomes]
rs2453168	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463016	0.88[EUR][1000 genomes]
rs2463017	0.88[EUR][1000 genomes]
rs2463019	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463025	0.88[EUR][1000 genomes]
rs2463429	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2463431	0.81[EUR][1000 genomes]
rs2463432	0.87[EUR][1000 genomes]
rs2463433	0.88[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2463441	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]
rs2463442	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463443	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2463444	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2468083	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468089	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[EUR][1000 genomes]
rs2468090	0.83[EUR][1000 genomes]
rs2468092	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2468099	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs2468100	0.88[EUR][1000 genomes]
rs2468105	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2468109	0.89[CEU][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2468340	0.84[EUR][1000 genomes]
rs2565167	0.88[EUR][1000 genomes]
rs2642110	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2642116	0.88[EUR][1000 genomes]
rs2730291	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2730295	0.82[EUR][1000 genomes]
rs2731030	0.82[EUR][1000 genomes]
rs4388976	0.95[CHB][hapmap]
rs4393404	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs6539167	0.81[EUR][1000 genomes]
rs6539170	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs6539171	0.88[CHB][hapmap]
rs703681	0.89[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs7135015	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs7138686	0.81[GIH][hapmap]
rs7847	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968763	0.84[CHB][hapmap]
rs7980681	0.86[EUR][1000 genomes]
rs903247	0.94[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2463018	CHST11	Cis_1M	lymphoblastoid	RTeQTL
rs2463018	HCFC2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105136800-105154400	Weak transcription	Right Ventricle	heart
2	chr12:105137200-105154000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:105137200-105157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:105141600-105155400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:105142400-105154600	Weak transcription	Fetal Brain Male	brain
6	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:105142800-105154800	Weak transcription	Fetal Brain Female	brain
9	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:105143600-105154200	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:105143800-105156800	Weak transcription	NHLF	lung
12	chr12:105143800-105160800	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:105144000-105158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:105144200-105154000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:105144200-105154000	Weak transcription	Left Ventricle	heart
16	chr12:105144200-105156800	Weak transcription	NHDF-Ad	bronchial
17	chr12:105144200-105157000	Weak transcription	NH-A	brain
18	chr12:105144200-105158000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:105145000-105153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:105145200-105154800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:105145200-105155600	Strong transcription	Dnd41	blood
22	chr12:105145200-105158200	Weak transcription	Adipose Nuclei	Adipose
23	chr12:105145400-105154200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:105145400-105161200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:105145600-105154800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:105145600-105162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:105145800-105161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:105145800-105161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:105145800-105161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:105146000-105161400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:105146800-105153400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:105146800-105156000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:105146800-105161200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:105148200-105154000	Weak transcription	HSMM	muscle
35	chr12:105148400-105154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:105148400-105156000	Weak transcription	Pancreas	Pancrea
37	chr12:105148800-105153800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:105149600-105157000	Weak transcription	HMEC	breast
39	chr12:105149800-105153600	Strong transcription	Fetal Thymus	thymus
40	chr12:105150000-105153000	Strong transcription	K562	blood
41	chr12:105150000-105154000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:105150000-105154000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:105150000-105154200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:105150000-105154400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:105150000-105155000	Strong transcription	Primary T cells from cord blood	blood
46	chr12:105150000-105155200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:105150000-105156000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:105150200-105153000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr12:105150200-105153000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:105150200-105154200	Strong transcription	Primary B cells from peripheral blood	blood

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