Variant report

Variant	rs2393111
Chromosome Location	chr12:117382290-117382291
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	chr12:117313964..117316353-chr12:117381200..117383712,2	MCF-7	breast:
2	chr12:117174363..117175916-chr12:117381728..117384041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction
ENSG00000135116	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10507277	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10507278	0.88[EUR][1000 genomes]
rs10732611	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10735099	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10735102	0.87[ASW][hapmap];0.94[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10735103	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10744885	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744886	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774891	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10774892	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774893	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774896	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10774898	0.81[ASW][hapmap]
rs10850731	0.92[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10850733	0.82[EUR][1000 genomes]
rs10850737	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10850741	0.82[EUR][1000 genomes]
rs10850743	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10850744	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs11068247	0.84[JPT][hapmap]
rs11068258	0.84[JPT][hapmap]
rs11068262	0.84[JPT][hapmap]
rs11068264	0.94[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11068277	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11068280	0.91[JPT][hapmap]
rs11068282	0.84[JPT][hapmap]
rs11068286	0.83[JPT][hapmap]
rs11068296	0.81[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11609970	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12299065	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs12821492	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823620	0.86[AMR][1000 genomes]
rs17583145	0.82[JPT][hapmap]
rs17616662	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2242469	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270794	0.80[TSI][hapmap]
rs2291916	0.81[ASW][hapmap]
rs2393110	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803089	0.84[JPT][hapmap]
rs3893370	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4074147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4076700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077519	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4130296	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4238051	0.81[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4299000	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4324001	0.81[ASN][1000 genomes]
rs4347476	0.84[JPT][hapmap]
rs4522274	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4542506	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4562925	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4562926	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4562927	0.87[ASW][hapmap];0.94[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4766812	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4766814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766815	0.87[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766818	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766820	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4766821	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4766822	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4766823	0.81[ASW][hapmap]
rs4767473	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4767474	0.87[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767476	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767477	0.81[ASW][hapmap]
rs4767478	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767480	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767482	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767483	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767484	0.87[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767485	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767487	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767488	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767489	0.87[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767490	0.81[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4767491	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767493	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6490097	0.81[ASN][1000 genomes]
rs6490102	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131746	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133066	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7133090	0.81[ASW][hapmap]
rs7136629	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7137006	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137752	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7297155	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297848	0.81[ASW][hapmap];0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7298447	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302025	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7303882	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308498	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7308734	0.88[EUR][1000 genomes]
rs7311972	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312388	0.80[ASN][1000 genomes]
rs7316144	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73403241	0.90[EUR][1000 genomes]
rs7484620	0.87[ASN][1000 genomes]
rs7487081	1.00[JPT][hapmap]
rs7952766	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954824	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958030	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7959666	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7962339	0.85[EUR][1000 genomes]
rs7973240	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7976815	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7977598	0.93[EUR][1000 genomes];0.84[ASN][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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1046811	chr12:117353904-117396230	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	esv1798657	chr12:117354067-117392259	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1048942	chr12:117365506-117400588	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2393111	C12orf49	cis	parietal	SCAN
rs2393111	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx
rs2393111	TESC	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117354800-117383200	Weak transcription	Esophagus	oesophagus
2	chr12:117358400-117392600	Weak transcription	Small Intestine	intestine
3	chr12:117363200-117399400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:117363400-117385000	Weak transcription	HUVEC	blood vessel
5	chr12:117365000-117383200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:117365000-117383400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:117365000-117406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:117365800-117383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:117366600-117383200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:117366600-117388400	Weak transcription	K562	blood
11	chr12:117367800-117382800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:117368000-117383200	Weak transcription	Hela-S3	cervix
13	chr12:117368000-117383400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:117368200-117383000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:117369800-117383200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:117371400-117383400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:117371400-117383400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:117372400-117383000	Weak transcription	NH-A	brain
19	chr12:117373000-117383200	Weak transcription	Fetal Brain Male	brain
20	chr12:117373400-117383200	Weak transcription	Right Ventricle	heart
21	chr12:117373800-117393200	Weak transcription	Stomach Mucosa	stomach
22	chr12:117374400-117385600	Weak transcription	NHDF-Ad	bronchial
23	chr12:117375000-117383200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:117375200-117382800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:117375400-117383200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:117375600-117383200	Weak transcription	Gastric	stomach
27	chr12:117376400-117383200	Weak transcription	Fetal Kidney	kidney
28	chr12:117376800-117383200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:117378000-117383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:117378000-117383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:117378000-117392600	Weak transcription	Psoas Muscle	Psoas
32	chr12:117378800-117382400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:117379000-117382400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:117379200-117383200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:117379400-117382400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:117379600-117383200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:117379800-117382400	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr12:117379800-117382600	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr12:117381000-117385400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:117381200-117382400	ZNF genes & repeats	Thymus	Thymus
41	chr12:117381200-117382600	Enhancers	Left Ventricle	heart
42	chr12:117381200-117385200	Strong transcription	HSMM	muscle
43	chr12:117381200-117390200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:117381200-117391200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:117381400-117382400	Enhancers	Pancreas	Pancrea
46	chr12:117381400-117382600	Enhancers	Adipose Nuclei	Adipose
47	chr12:117381400-117383000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:117381400-117383000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:117381400-117383200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:117381400-117383200	Weak transcription	NHEK	skin

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