Variant report

Variant	rs7973240
Chromosome Location	chr12:117408148-117408149
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	chr12:117406724..117409328-chr12:117437750..117440226,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10507277	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10507278	0.89[EUR][1000 genomes]
rs10732611	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735099	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735102	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs10735103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744885	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10744886	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10774891	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10774892	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10774893	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774896	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10850731	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs10850737	0.82[EUR][1000 genomes]
rs10850741	0.80[EUR][1000 genomes]
rs10850743	0.94[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10850744	0.93[CEU][hapmap];0.94[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];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11068277	0.94[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11068280	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs11068282	0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11068286	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs11068296	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12299065	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs12821492	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17583145	0.82[JPT][hapmap]
rs17616662	0.84[JPT][hapmap]
rs2242469	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270794	0.80[TSI][hapmap]
rs2393110	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2393111	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]
rs35833140	0.81[ASN][1000 genomes]
rs3803089	0.84[JPT][hapmap]
rs3893370	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4074147	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4076700	1.00[CEU][hapmap];0.88[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];0.90[ASN][1000 genomes]
rs4077519	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4130296	0.93[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238051	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs4299000	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4324001	0.83[ASN][1000 genomes]
rs4347476	0.84[JPT][hapmap]
rs4522274	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4542506	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562925	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4562926	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4562927	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4766812	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4766814	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766815	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766818	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4766820	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766821	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4766822	0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs4767473	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4767474	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767476	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767478	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767480	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767482	0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767483	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767484	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767485	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767487	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767488	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767489	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767490	0.81[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs4767491	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767493	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6490097	0.83[ASN][1000 genomes]
rs6490102	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131746	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133066	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7136629	0.84[JPT][hapmap]
rs7137006	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137752	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297155	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297848	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs7297934	0.81[ASN][1000 genomes]
rs7298447	0.93[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302025	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7303882	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308734	0.89[EUR][1000 genomes]
rs7311972	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312388	0.82[ASN][1000 genomes]
rs7316144	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73403241	0.91[EUR][1000 genomes]
rs7484620	0.89[ASN][1000 genomes]
rs7487081	1.00[JPT][hapmap]
rs7952766	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7954824	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958030	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959666	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962339	0.86[EUR][1000 genomes]
rs7976815	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7977598	0.93[EUR][1000 genomes];0.93[ASN][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	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	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7973240	TESC	cis	parietal	SCAN
rs7973240	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx
rs7973240	HRK	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117384400-117411200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:117384600-117427400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:117384800-117411000	Weak transcription	Hela-S3	cervix
4	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:117385200-117410200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:117385200-117410600	Weak transcription	Fetal Kidney	kidney
7	chr12:117385800-117408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:117387800-117463600	Weak transcription	HMEC	breast
9	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
10	chr12:117394600-117415400	Weak transcription	HSMMtube	muscle
11	chr12:117397000-117429200	Weak transcription	Right Ventricle	heart
12	chr12:117397000-117442400	Weak transcription	Colonic Mucosa	Colon
13	chr12:117397200-117410400	Weak transcription	Pancreas	Pancrea
14	chr12:117398000-117409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:117398200-117417400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:117400400-117412000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:117400400-117417800	Weak transcription	K562	blood
18	chr12:117400800-117415400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:117401000-117409000	Weak transcription	GM12878-XiMat	blood
20	chr12:117401400-117408200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:117401600-117408400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:117401600-117408400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:117401600-117408800	Strong transcription	Primary T cells from cord blood	blood
24	chr12:117402200-117408200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:117402200-117408400	Strong transcription	Placenta	Placenta
26	chr12:117402200-117417200	Weak transcription	Stomach Mucosa	stomach
27	chr12:117402400-117408200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:117402600-117411200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:117402800-117408200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:117403000-117412200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:117403400-117410400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:117403400-117416800	Weak transcription	HUVEC	blood vessel
33	chr12:117403400-117418000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:117403400-117423200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:117403600-117410600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:117403600-117413200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:117403600-117420400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:117404400-117409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:117404600-117410400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:117404600-117410400	Weak transcription	Esophagus	oesophagus
41	chr12:117404600-117410400	Weak transcription	NHEK	skin
42	chr12:117404600-117427000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:117404600-117442400	Weak transcription	HepG2	liver
44	chr12:117404800-117410400	Weak transcription	Lung	lung
45	chr12:117404800-117426400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:117405000-117411000	Weak transcription	Fetal Thymus	thymus
47	chr12:117405200-117410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:117405400-117408200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:117405400-117409000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:117405400-117410200	Weak transcription	Duodenum Mucosa	Duodenum

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