Variant report

Variant	rs10850743
Chromosome Location	chr12:117462785-117462786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117461681..117464080-chr12:117470751..117473024,2	MCF-7	breast:
2	chr12:117462019..117462826-chr12:117557173..117558198,3	MCF-7	breast:
3	chr12:117461340..117464538-chr12:117578917..117582364,3	MCF-7	breast:
4	chr12:117462662..117464720-chr12:117586991..117588878,2	MCF-7	breast:
5	chr12:117455374..117458365-chr12:117461422..117463402,2	MCF-7	breast:
6	chr12:117462045..117463688-chr12:117467328..117470013,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10507277	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10507278	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs10732611	0.87[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735099	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735102	0.80[ASW][hapmap];1.00[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10735103	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744885	0.83[EUR][1000 genomes]
rs10744886	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10774891	0.86[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap]
rs10774892	0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10774893	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10774896	0.87[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10850731	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10850737	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10850741	0.81[EUR][1000 genomes]
rs10850744	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11068245	0.87[CHB][hapmap]
rs11068247	0.87[CHB][hapmap]
rs11068258	0.80[CHB][hapmap]
rs11068264	1.00[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11068277	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11068280	0.86[CHB][hapmap]
rs11068282	0.87[CHB][hapmap]
rs11068286	0.86[CHB][hapmap]
rs11068292	0.94[YRI][hapmap]
rs11068296	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299065	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12821492	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17616662	0.80[CHB][hapmap]
rs2242469	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270794	0.81[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs2393110	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2393111	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]
rs3782189	0.80[CHB][hapmap]
rs3782190	0.80[CHB][hapmap]
rs3893370	0.94[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4074147	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4076700	0.94[CEU][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]
rs4077519	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130296	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4238051	0.83[TSI][hapmap]
rs4299000	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4522274	0.86[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4542506	0.94[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4562925	0.87[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4562926	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4562927	0.80[ASW][hapmap];1.00[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4766812	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766814	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4766815	0.80[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4766818	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766820	0.87[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4766821	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4766822	0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767473	0.83[TSI][hapmap]
rs4767474	0.80[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4767476	0.87[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4767478	0.93[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767480	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4767482	0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767483	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767484	0.80[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767485	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767487	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767488	0.88[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4767489	0.80[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767490	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4767491	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767493	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60940473	0.83[EUR][1000 genomes]
rs6490102	0.87[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7131746	0.94[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7133066	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs7136629	0.86[CHB][hapmap]
rs7137006	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7137752	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7297155	0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297446	0.81[CHB][hapmap]
rs7297848	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7298447	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302025	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7303882	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308498	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308734	0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7311972	0.87[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7316144	0.93[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73403241	0.96[EUR][1000 genomes]
rs7487081	0.86[JPT][hapmap]
rs7952766	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7954824	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7957907	0.83[EUR][1000 genomes]
rs7958030	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7959666	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7962339	0.92[EUR][1000 genomes]
rs7973240	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]
rs7976815	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7977598	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9804817	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10850743	C12orf49	cis	parietal	SCAN
rs10850743	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx
rs10850743	HRK	cis	multi-tissue	Pritchard
rs10850743	TESC	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117387800-117463600	Weak transcription	HMEC	breast
2	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
3	chr12:117426200-117466600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:117444000-117462800	Weak transcription	K562	blood
5	chr12:117452400-117463400	Strong transcription	Fetal Intestine Large	intestine
6	chr12:117452400-117463800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:117452400-117469000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:117452600-117463600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:117452800-117463200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:117452800-117463200	Strong transcription	A549	lung
11	chr12:117452800-117465200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:117452800-117468400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:117452800-117470200	Weak transcription	HUVEC	blood vessel
14	chr12:117452800-117479000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:117453200-117463600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:117453600-117463200	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:117453600-117470600	Weak transcription	Psoas Muscle	Psoas
18	chr12:117454000-117463200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:117454200-117462800	Weak transcription	NH-A	brain
20	chr12:117454200-117463000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:117454800-117466600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:117454800-117468600	Strong transcription	Primary B cells from cord blood	blood
23	chr12:117455600-117463200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:117455600-117463600	Strong transcription	Fetal Stomach	stomach
25	chr12:117456200-117466800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:117456400-117463400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:117456600-117465400	Weak transcription	Aorta	Aorta
28	chr12:117456800-117468000	Strong transcription	Liver	Liver
29	chr12:117457200-117469200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:117457600-117463600	Strong transcription	HepG2	liver
31	chr12:117457600-117469200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:117457800-117468200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:117458000-117463400	Strong transcription	Dnd41	blood
34	chr12:117458200-117463400	Strong transcription	Primary T cells from cord blood	blood
35	chr12:117458600-117463200	Strong transcription	Pancreas	Pancrea
36	chr12:117458600-117463400	Weak transcription	Fetal Brain Male	brain
37	chr12:117458600-117469200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:117458800-117469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:117459000-117463200	Weak transcription	Fetal Heart	heart
40	chr12:117459200-117463600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:117459600-117469200	Strong transcription	Osteobl	bone
42	chr12:117459800-117463600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:117460200-117463600	Strong transcription	Fetal Lung	lung
44	chr12:117460400-117463200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:117460600-117463400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:117460800-117463400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:117460800-117463600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:117460800-117468000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:117461000-117462800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:117461000-117463200	Strong transcription	Adipose Nuclei	Adipose

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