Variant report

Variant	rs2642109
Chromosome Location	chr12:105156951-105156952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105156899..105157460-chr12:105169554..105170172,2	MCF-7	breast:
2	chr12:105154675..105157648-chr12:105161416..105163979,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.85[GIH][hapmap]
rs1038968	0.87[EUR][1000 genomes]
rs10507184	0.89[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs1070316	0.83[CEU][hapmap]
rs1155994	0.89[CEU][hapmap]
rs1316594	0.81[EUR][1000 genomes]
rs1389610	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1389611	0.88[EUR][1000 genomes]
rs1389612	0.89[CEU][hapmap]
rs1474459	1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[EUR][1000 genomes]
rs1565813	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs1565815	0.81[EUR][1000 genomes]
rs2004806	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047124	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2088019	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2131806	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2245927	0.81[EUR][1000 genomes]
rs2245929	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245931	0.81[EUR][1000 genomes]
rs2248012	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs2453154	0.94[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453155	0.94[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs2453156	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2453161	0.89[CEU][hapmap]
rs2453166	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs2453167	0.81[EUR][1000 genomes]
rs2463016	0.81[EUR][1000 genomes]
rs2463017	0.81[EUR][1000 genomes]
rs2463018	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs2463019	0.89[CEU][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes]
rs2463020	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2463025	0.81[EUR][1000 genomes]
rs2463431	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2463432	0.80[EUR][1000 genomes]
rs2463433	0.81[EUR][1000 genomes]
rs2463434	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2463435	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2463440	0.94[CEU][hapmap]
rs2463441	0.89[CEU][hapmap]
rs2463442	0.94[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs2463443	0.94[CEU][hapmap]
rs2463444	0.94[CEU][hapmap]
rs2468082	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468089	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs2468099	0.89[CEU][hapmap]
rs2468105	0.89[CEU][hapmap]
rs2468109	0.89[CEU][hapmap]
rs2468110	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs2468112	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2565167	0.81[EUR][1000 genomes]
rs2642116	0.81[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.85[GIH][hapmap]
rs2730295	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2731030	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6539167	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6539170	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs703681	0.89[CEU][hapmap]
rs903247	0.94[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv560052	chr12:105155815-105157975	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2642109	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105137200-105157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:105142400-105160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:105142600-105158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:105142800-105158200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:105143800-105160800	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:105144000-105158200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:105144200-105157000	Weak transcription	NH-A	brain
8	chr12:105144200-105158000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:105145200-105158200	Weak transcription	Adipose Nuclei	Adipose
10	chr12:105145400-105161200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:105145600-105162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:105145800-105161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:105145800-105161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:105145800-105161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:105146000-105161400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:105146800-105161200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:105149600-105157000	Weak transcription	HMEC	breast
18	chr12:105151400-105158400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:105151400-105161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:105151600-105157000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:105151600-105157000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:105151600-105157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:105151600-105157000	Weak transcription	A549	lung
24	chr12:105151600-105157400	Weak transcription	HSMMtube	muscle
25	chr12:105151600-105158400	Weak transcription	Ovary	ovary
26	chr12:105151600-105160800	Weak transcription	Esophagus	oesophagus
27	chr12:105151600-105161800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:105151600-105162800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:105151800-105157000	Weak transcription	Osteobl	bone
30	chr12:105152200-105158000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:105152400-105162600	Weak transcription	Brain Anterior Caudate	brain
32	chr12:105152600-105158000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:105152600-105158400	Weak transcription	Placenta	Placenta
34	chr12:105152800-105157000	Weak transcription	Spleen	Spleen
35	chr12:105153000-105157000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:105153000-105157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:105153000-105157000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:105153000-105157000	Weak transcription	Lung	lung
39	chr12:105153000-105157000	Weak transcription	K562	blood
40	chr12:105153000-105157000	Weak transcription	NHEK	skin
41	chr12:105153000-105157200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:105153000-105157200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:105153000-105157200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:105153000-105158000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:105153000-105158000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:105153200-105161800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:105153600-105158000	Weak transcription	Fetal Thymus	thymus
48	chr12:105153800-105158000	Weak transcription	Thymus	Thymus
49	chr12:105154000-105158200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:105154200-105157200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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