Variant report

Variant	rs4073998
Chromosome Location	chr12:50038292-50038293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50036454..50040797-chr12:50041682..50045793,5	MCF-7	breast:
2	chr12:50037838..50040032-chr12:50221476..50224134,2	K562	blood:
3	chr12:50030175..50032121-chr12:50038039..50040116,2	K562	blood:
4	chr12:50037386..50039207-chr12:50100463..50102234,32	MCF-7	breast:
5	chr12:50038061..50038962-chr12:50170097..50170756,2	K562	blood:
6	chr12:50036595..50042102-chr12:50135109..50139790,7	K562	blood:
7	chr12:50038061..50039763-chr12:50138977..50140506,2	K562	blood:
8	chr12:50033388..50039946-chr12:50098324..50104633,12	K562	blood:
9	chr12:50034899..50039875-chr12:50099580..50104040,10	MCF-7	breast:
10	chr12:50029309..50033089-chr12:50034924..50039284,4	MCF-7	breast:
11	chr12:50037981..50041793-chr12:50133371..50136626,3	K562	blood:
12	chr12:50037543..50040518-chr12:50041058..50044921,6	K562	blood:
13	chr12:50037720..50039414-chr12:50100730..50101951,24	K562	blood:
14	chr12:50038060..50038596-chr12:50134612..50135520,2	K562	blood:
15	chr12:50038039..50038598-chr16:25122994..25123747,2	MCF-7	breast:
16	chr12:50038093..50038993-chr12:50171692..50172608,3	MCF-7	breast:
17	chr12:50017303..50019793-chr12:50037938..50040749,2	K562	blood:
18	chr12:50037513..50040082-chr12:50144321..50146045,2	K562	blood:
19	chr12:50035440..50045362-chr12:50096806..50104789,13	K562	blood:
20	chr12:50037476..50040011-chr12:50080826..50083023,2	MCF-7	breast:
21	chr12:50036525..50042244-chr12:50133880..50137452,9	MCF-7	breast:
22	chr12:50036570..50040051-chr12:50043792..50046609,5	MCF-7	breast:
23	chr12:50038265..50040146-chr12:50124251..50126036,2	K562	blood:
24	chr12:50038102..50038980-chr12:50171749..50172585,3	K562	blood:
25	chr12:50038069..50038917-chr12:50156600..50157435,3	MCF-7	breast:
26	chr12:50038060..50039002-chr12:50156488..50157485,2	K562	blood:
27	chr12:50014216..50017582-chr12:50033050..50038779,6	MCF-7	breast:
28	chr12:50038224..50039191-chr12:50232599..50233420,2	MCF-7	breast:
29	chr12:50037973..50039228-chr12:50100886..50102456,37	MCF-7	breast:
30	chr12:50034541..50040504-chr12:50134095..50137099,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110844	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000205629	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000257570	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1049986	0.82[JPT][hapmap]
rs10875964	0.82[AMR][1000 genomes]
rs10875968	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169065	1.00[JPT][hapmap]
rs11169069	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169070	0.85[AMR][1000 genomes]
rs11169073	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169076	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11169081	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169082	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169092	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11169097	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11169101	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169104	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs11169106	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs11169140	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1150057	1.00[JPT][hapmap]
rs11615488	0.84[ASN][1000 genomes]
rs11833411	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11834380	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs12299505	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12299513	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12303310	0.82[JPT][hapmap]
rs12305460	0.80[AMR][1000 genomes]
rs12310510	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs12311839	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12314878	0.81[ASN][1000 genomes]
rs12316284	0.82[JPT][hapmap]
rs12317646	0.82[AMR][1000 genomes]
rs12320556	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12321819	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13066	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13906	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1470906	0.82[JPT][hapmap]
rs1574326	0.82[JPT][hapmap]
rs17123808	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs17123981	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs1902329	1.00[JPT][hapmap]
rs1902330	0.82[JPT][hapmap]
rs2005195	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2241418	0.81[ASN][1000 genomes]
rs2278068	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2278069	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2278070	0.84[ASN][1000 genomes]
rs2303305	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2336058	0.82[JPT][hapmap]
rs2878532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815832	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3887727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3887728	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4045193	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4133070	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs4563	0.82[JPT][hapmap]
rs4584654	0.82[JPT][hapmap]
rs52824916	0.84[ASN][1000 genomes]
rs55853522	0.81[ASN][1000 genomes]
rs57916875	0.84[ASN][1000 genomes]
rs58278271	0.89[ASN][1000 genomes]
rs59233136	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59940006	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60402517	0.80[AMR][1000 genomes]
rs61512987	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61616163	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580719	0.82[AMR][1000 genomes]
rs7131915	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7132792	0.82[JPT][hapmap]
rs7133398	1.00[CHB][hapmap]
rs7137976	0.82[JPT][hapmap]
rs7296281	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7299609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes]
rs7301209	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7306877	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7309607	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7312658	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73305008	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73305012	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73306808	0.82[AMR][1000 genomes]
rs7688	0.82[JPT][hapmap]
rs7952734	0.82[JPT][hapmap]
rs7952938	0.89[ASN][1000 genomes]
rs7953911	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7954994	0.82[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs7955586	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs7956181	0.82[JPT][hapmap]
rs7962863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7963954	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7965658	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7970241	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7973389	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7975599	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7975712	1.00[CHB][hapmap]
rs7977389	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7979262	0.82[AMR][1000 genomes]
rs7979285	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs876889	0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs897056	0.85[AMR][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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50017800-50042200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:50018000-50043000	Weak transcription	Psoas Muscle	Psoas
3	chr12:50030800-50038400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:50030800-50057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:50031200-50038400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:50031200-50038600	Strong transcription	Fetal Intestine Large	intestine
7	chr12:50031200-50045600	Weak transcription	Small Intestine	intestine
8	chr12:50031400-50041800	Weak transcription	Fetal Brain Male	brain
9	chr12:50031600-50052200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:50031800-50038600	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:50031800-50056200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:50032000-50038600	Weak transcription	Fetal Heart	heart
13	chr12:50033200-50052600	Strong transcription	Brain Germinal Matrix	brain
14	chr12:50033600-50041000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:50033800-50039000	Strong transcription	Gastric	stomach
16	chr12:50033800-50048800	Strong transcription	Fetal Brain Female	brain
17	chr12:50034000-50038600	Strong transcription	Brain Angular Gyrus	brain
18	chr12:50034000-50038600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50034000-50040000	Strong transcription	Aorta	Aorta
20	chr12:50034200-50038600	Strong transcription	Brain Anterior Caudate	brain
21	chr12:50034200-50045000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr12:50034200-50045800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:50034200-50053000	Strong transcription	NHLF	lung
24	chr12:50034200-50056200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:50034400-50040800	Strong transcription	Pancreas	Pancrea
26	chr12:50034600-50045200	Strong transcription	Osteobl	bone
27	chr12:50034800-50038600	Strong transcription	Lung	lung
28	chr12:50034800-50041200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:50034800-50042400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:50034800-50044400	Genic enhancers	Placenta	Placenta
31	chr12:50034800-50056400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:50034800-50056600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:50035200-50038800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:50035400-50038600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:50035400-50038600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:50035400-50038800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:50035400-50045200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:50035600-50038600	Genic enhancers	NHEK	skin
39	chr12:50035600-50049800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:50035600-50055000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr12:50035600-50056400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:50035800-50038400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:50035800-50038600	Strong transcription	Ovary	ovary
44	chr12:50035800-50038600	Strong transcription	Spleen	Spleen
45	chr12:50035800-50038800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:50035800-50040800	Strong transcription	HSMMtube	muscle
47	chr12:50035800-50048800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr12:50036000-50038400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:50036000-50038600	Strong transcription	Fetal Lung	lung
50	chr12:50036000-50039400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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