Variant report

Variant	rs7297848
Chromosome Location	chr12:117443591-117443592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117441591..117444664-chr12:117447106..117450120,5	MCF-7	breast:
2	chr12:117437746..117440229-chr12:117441303..117443639,2	K562	blood:
3	chr12:117442448..117444268-chr12:117445719..117447453,2	K562	blood:
4	chr12:117442427..117445023-chr12:117448481..117451118,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10507277	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10507278	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs10732611	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10735099	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10735102	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735103	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744885	0.82[AMR][1000 genomes]
rs10744886	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10774891	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs10774892	0.86[JPT][hapmap]
rs10774896	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs10774898	0.87[ASW][hapmap]
rs10850731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10850737	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10850743	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]
rs10850744	0.93[CEU][hapmap]
rs11068264	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068277	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12823620	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16947281	0.94[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2242469	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2270794	0.81[CEU][hapmap]
rs2291916	0.87[ASW][hapmap]
rs2393111	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]
rs3893370	0.94[CEU][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs4074147	0.86[JPT][hapmap]
rs4076700	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]
rs4077519	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4130296	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs4522274	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs4542506	0.94[CEU][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4562925	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs4562926	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4562927	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4766812	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4766814	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4766815	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4766820	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs4766821	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4766822	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4766823	0.87[ASW][hapmap]
rs4767474	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4767476	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs4767477	0.87[ASW][hapmap]
rs4767478	0.93[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4767480	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4767483	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs4767484	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767485	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4767487	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767488	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4767489	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767491	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767493	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6490102	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7131746	0.94[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7133066	0.85[JPT][hapmap]
rs7133090	0.87[ASW][hapmap]
rs7137006	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7137752	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7297155	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7298447	0.87[CEU][hapmap]
rs7303882	0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308498	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7308734	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311972	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs7316144	0.93[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73403241	0.91[EUR][1000 genomes]
rs7487081	0.86[JPT][hapmap]
rs7958030	0.92[EUR][1000 genomes]
rs7959666	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7962339	0.87[EUR][1000 genomes]
rs7973240	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs7977598	0.93[AMR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7297848	C12orf49	cis	parietal	SCAN
rs7297848	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx
rs7297848	TESC	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:117387800-117463600	Weak transcription	HMEC	breast
3	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
4	chr12:117408400-117452200	Weak transcription	Thymus	Thymus
5	chr12:117411600-117451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:117417200-117452400	Weak transcription	Psoas Muscle	Psoas
7	chr12:117417400-117453600	Weak transcription	GM12878-XiMat	blood
8	chr12:117418400-117444600	Weak transcription	HUVEC	blood vessel
9	chr12:117426200-117466600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:117426800-117445600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:117428200-117447600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:117432000-117446200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:117432200-117444200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:117432200-117446400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:117432600-117445800	Strong transcription	Fetal Muscle Leg	muscle
16	chr12:117432800-117444600	Strong transcription	Fetal Stomach	stomach
17	chr12:117434200-117449800	Weak transcription	NHEK	skin
18	chr12:117434800-117444200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:117435600-117449800	Weak transcription	Stomach Mucosa	stomach
20	chr12:117436800-117445600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:117437000-117447800	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:117437400-117451600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:117437600-117445800	Strong transcription	Primary B cells from cord blood	blood
24	chr12:117437600-117447000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:117437600-117448000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:117438000-117445600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:117438200-117444800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:117438200-117445600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:117438200-117445800	Strong transcription	Primary T cells from cord blood	blood
30	chr12:117438200-117447600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:117438600-117446200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:117438800-117445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:117439000-117445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:117439200-117447000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:117439200-117447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:117439400-117444600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:117439400-117445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:117440000-117444600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:117440400-117452200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:117440800-117446000	Strong transcription	HSMM	muscle
41	chr12:117441000-117444400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr12:117441000-117444600	Strong transcription	Fetal Intestine Large	intestine
43	chr12:117441200-117449800	Weak transcription	Right Atrium	heart
44	chr12:117441200-117451200	Weak transcription	Fetal Brain Female	brain
45	chr12:117441800-117444400	Strong transcription	Gastric	stomach
46	chr12:117441800-117444800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:117441800-117445800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:117441800-117445800	Strong transcription	Osteobl	bone
49	chr12:117441800-117446000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:117441800-117446600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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