Variant report

Variant	rs7302025
Chromosome Location	chr12:117442902-117442903
allele	A/G
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: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10507277	0.83[EUR][1000 genomes]
rs10507278	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10732611	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10735103	0.82[EUR][1000 genomes]
rs10774891	0.85[CEU][hapmap]
rs10774892	0.90[EUR][1000 genomes]
rs10774893	0.92[EUR][1000 genomes]
rs10774896	0.86[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs10850733	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850741	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850743	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10850744	0.85[CEU][hapmap]
rs11068296	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11838192	0.89[ASN][1000 genomes]
rs12299065	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302906	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16947275	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2173653	1.00[JPT][hapmap]
rs2242469	0.81[EUR][1000 genomes]
rs2270794	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2393110	0.90[EUR][1000 genomes]
rs2393111	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs3782193	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs3893370	0.81[CEU][hapmap]
rs4074147	0.94[EUR][1000 genomes]
rs4076700	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs4130296	0.86[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs4238051	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4299000	0.92[EUR][1000 genomes]
rs4522274	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs4542506	0.81[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4562925	0.86[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs4766815	0.83[TSI][hapmap]
rs4766818	0.94[EUR][1000 genomes]
rs4766820	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs4766821	0.81[EUR][1000 genomes]
rs4767473	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767474	0.83[TSI][hapmap]
rs4767476	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs4767482	0.94[EUR][1000 genomes]
rs4767483	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs4767484	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4767485	0.82[EUR][1000 genomes]
rs4767487	0.81[EUR][1000 genomes]
rs4767489	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4767490	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767491	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4767493	0.82[EUR][1000 genomes]
rs59348125	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60940473	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490101	1.00[JPT][hapmap]
rs6490102	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs7131746	0.81[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7137752	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7297155	0.81[EUR][1000 genomes]
rs7298447	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs7303752	0.85[EUR][1000 genomes]
rs7307907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308498	0.81[EUR][1000 genomes]
rs7311972	0.86[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs7316144	0.81[EUR][1000 genomes]
rs73403241	0.86[EUR][1000 genomes]
rs73405256	0.89[ASN][1000 genomes]
rs7952766	0.90[EUR][1000 genomes]
rs7954600	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954824	0.94[EUR][1000 genomes]
rs7957907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958030	0.82[EUR][1000 genomes]
rs7959666	0.83[EUR][1000 genomes]
rs7960610	1.00[JPT][hapmap]
rs7962339	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973240	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7973925	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976815	0.90[EUR][1000 genomes]
rs7977598	0.82[EUR][1000 genomes]
rs7978725	0.84[ASN][1000 genomes]
rs7979277	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9804817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs987560	1.00[JPT][hapmap]

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
rs7302025	TESC	cis	parietal	SCAN
rs7302025	HRK	cis	multi-tissue	Pritchard
rs7302025	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

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	chr12:117427800-117443400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:117428200-117447600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:117432000-117446200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:117432200-117444200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:117432200-117446400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:117432600-117445800	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:117432800-117444600	Strong transcription	Fetal Stomach	stomach
18	chr12:117434200-117443200	Weak transcription	Hela-S3	cervix
19	chr12:117434200-117449800	Weak transcription	NHEK	skin
20	chr12:117434800-117443000	Weak transcription	Brain Anterior Caudate	brain
21	chr12:117434800-117444200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:117435600-117449800	Weak transcription	Stomach Mucosa	stomach
23	chr12:117436800-117445600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:117437000-117447800	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:117437400-117451600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:117437600-117445800	Strong transcription	Primary B cells from cord blood	blood
27	chr12:117437600-117447000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:117437600-117448000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:117438000-117443200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:117438000-117445600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:117438200-117444800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:117438200-117445600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:117438200-117445800	Strong transcription	Primary T cells from cord blood	blood
34	chr12:117438200-117447600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:117438600-117446200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:117438800-117445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:117439000-117445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:117439200-117447000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:117439200-117447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:117439400-117443400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:117439400-117444600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:117439400-117445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:117440000-117444600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:117440200-117443200	Weak transcription	Brain Angular Gyrus	brain
45	chr12:117440400-117443200	Weak transcription	Right Ventricle	heart
46	chr12:117440400-117452200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:117440800-117443000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:117440800-117446000	Strong transcription	HSMM	muscle
49	chr12:117441000-117443000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr12:117441000-117444400	Strong transcription	Brain Inferior Temporal Lobe	brain

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