Variant report

Variant	rs12173347
Chromosome Location	chr6:35339000-35339001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35335918..35340012-chr6:35342665..35344421,4	K562	blood:
2	chr6:35337473..35339598-chr6:35358141..35360010,2	K562	blood:
3	chr6:35330201..35332788-chr6:35338848..35341376,3	K562	blood:
4	chr6:35337130..35339523-chr6:35342584..35344904,3	MCF-7	breast:
5	chr6:35335918..35339865-chr6:35340596..35344421,5	K562	blood:
6	chr6:35335380..35337947-chr6:35338128..35341057,2	MCF-7	breast:
7	chr6:35329439..35333357-chr6:35335770..35342563,9	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10080361	0.82[ASN][1000 genomes]
rs10080411	0.82[ASN][1000 genomes]
rs1013907	0.82[ASN][1000 genomes]
rs1034449	1.00[YRI][hapmap]
rs10947540	0.83[ASN][1000 genomes]
rs1194	0.84[ASN][1000 genomes]
rs12173582	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211765	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12211943	0.83[ASN][1000 genomes]
rs13214290	0.81[ASN][1000 genomes]
rs1888823	0.84[ASN][1000 genomes]
rs1888824	0.83[ASN][1000 genomes]
rs1888825	0.83[ASN][1000 genomes]
rs1894650	0.83[ASN][1000 genomes]
rs1894651	0.82[ASN][1000 genomes]
rs1894652	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1894653	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1929847	0.84[ASN][1000 genomes]
rs1929849	0.81[ASN][1000 genomes]
rs2032538	1.00[CEU][hapmap]
rs2183834	0.88[ASN][1000 genomes]
rs2267658	0.82[ASN][1000 genomes]
rs2267660	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267661	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267662	0.84[ASN][1000 genomes]
rs2267663	0.83[ASN][1000 genomes]
rs2267664	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284195	0.83[ASN][1000 genomes]
rs2284196	0.82[ASN][1000 genomes]
rs2395621	0.84[ASN][1000 genomes]
rs3777744	0.82[ASN][1000 genomes]
rs3798342	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3798343	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800382	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3800383	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800385	0.81[ASN][1000 genomes]
rs3800386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800388	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800392	0.81[ASN][1000 genomes]
rs3800400	0.89[EUR][1000 genomes]
rs4583983	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711409	0.82[ASN][1000 genomes]
rs4711411	0.83[ASN][1000 genomes]
rs4711413	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711414	0.84[ASN][1000 genomes]
rs4713845	0.83[ASN][1000 genomes]
rs4713848	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713850	0.83[ASN][1000 genomes]
rs4713853	0.82[ASN][1000 genomes]
rs58925593	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62403575	0.84[ASN][1000 genomes]
rs6902523	0.84[ASN][1000 genomes]
rs6907324	0.84[ASN][1000 genomes]
rs6907573	0.88[ASN][1000 genomes]
rs6913037	0.83[ASN][1000 genomes]
rs6913475	0.80[ASN][1000 genomes]
rs6920747	0.84[ASN][1000 genomes]
rs6928769	0.81[ASN][1000 genomes]
rs6938946	0.86[ASN][1000 genomes]
rs72909061	0.81[ASN][1000 genomes]
rs7757316	0.81[ASN][1000 genomes]
rs7763946	0.81[ASN][1000 genomes]
rs7769906	0.83[ASN][1000 genomes]
rs7772212	0.84[ASN][1000 genomes]
rs9296144	0.83[ASN][1000 genomes]
rs9296150	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348974	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366883	0.83[ASN][1000 genomes]
rs9366885	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368852	0.89[EUR][1000 genomes]
rs9368853	0.89[EUR][1000 genomes]
rs9368854	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368857	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368859	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368860	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368865	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380501	0.84[ASN][1000 genomes]
rs9380502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380505	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380507	1.00[EUR][1000 genomes]
rs9394283	0.81[ASN][1000 genomes]
rs9394289	0.83[ASN][1000 genomes]
rs9462072	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9469964	0.81[ASN][1000 genomes]
rs9469979	0.82[ASN][1000 genomes]
rs9469997	0.83[ASN][1000 genomes]
rs9469998	0.81[ASN][1000 genomes]
rs975496	0.84[ASN][1000 genomes]
rs991145	0.83[ASN][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	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35321000-35342400	Weak transcription	Fetal Kidney	kidney
2	chr6:35328400-35344800	Weak transcription	Fetal Lung	lung
3	chr6:35329000-35350800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:35331200-35350800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:35331400-35339200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:35331600-35345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:35331600-35345400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:35334200-35339800	Enhancers	K562	blood
9	chr6:35334800-35339400	Enhancers	Psoas Muscle	Psoas
10	chr6:35335000-35339800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:35335400-35339400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:35335400-35339800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:35335400-35339800	Enhancers	Adipose Nuclei	Adipose
14	chr6:35335400-35340000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr6:35335600-35339000	Enhancers	Hela-S3	cervix
16	chr6:35335600-35339200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:35335600-35339400	Enhancers	Small Intestine	intestine
18	chr6:35335600-35339400	Enhancers	Dnd41	blood
19	chr6:35335600-35339800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:35335800-35339600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:35335800-35340000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:35335800-35340400	Enhancers	Spleen	Spleen
23	chr6:35336000-35339200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:35336000-35339400	Enhancers	NHLF	lung
25	chr6:35336000-35339600	Enhancers	Fetal Thymus	thymus
26	chr6:35336000-35339600	Enhancers	HMEC	breast
27	chr6:35336000-35339800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:35336000-35339800	Enhancers	HUVEC	blood vessel
29	chr6:35336200-35339400	Flanking Active TSS	GM12878-XiMat	blood
30	chr6:35336200-35339600	Enhancers	Placenta	Placenta
31	chr6:35336200-35340000	Enhancers	Primary B cells from peripheral blood	blood
32	chr6:35336400-35339400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:35336600-35339600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:35336600-35339600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:35337200-35339800	Enhancers	Lung	lung
36	chr6:35337200-35339800	Enhancers	Right Ventricle	heart
37	chr6:35337200-35339800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr6:35337200-35341400	Enhancers	Brain Hippocampus Middle	brain
39	chr6:35337400-35339000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:35337400-35339400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:35337400-35339600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:35337400-35339800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:35337600-35339000	Enhancers	Colonic Mucosa	Colon
44	chr6:35337800-35339200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:35337800-35339200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:35337800-35339200	Enhancers	Esophagus	oesophagus
47	chr6:35337800-35339200	Enhancers	Left Ventricle	heart
48	chr6:35337800-35339400	Enhancers	Fetal Muscle Leg	muscle
49	chr6:35337800-35339400	Enhancers	Right Atrium	heart
50	chr6:35337800-35339600	Enhancers	Primary hematopoietic stem cells	blood

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