Variant report

Variant	rs12523978
Chromosome Location	chr6:163857805-163857806
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163849473..163851849-chr6:163857419..163859004,2	K562	blood:
2	chr6:163852314..163854310-chr6:163857070..163858780,2	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10080505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12523713	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17176494	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4112651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60332904	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6455905	0.90[EUR][1000 genomes]
rs6901592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6902608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6906081	0.85[EUR][1000 genomes]
rs6906275	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6906725	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6910323	0.96[EUR][1000 genomes]
rs6914093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6917030	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6928869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6936927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6937072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6937097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73013516	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73013528	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73013553	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73015316	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7748261	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7759606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7761090	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7770852	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9456868	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9458821	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9458823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9458825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9458827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9458828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9458830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9458837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9458849	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9458857	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9458859	0.90[EUR][1000 genomes]
rs9654569	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
4	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
7	chr6:163843800-163862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:163844200-163860400	Weak transcription	Lung	lung
9	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:163846000-163861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:163846400-163860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:163847800-163862400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:163847800-163862600	Weak transcription	Aorta	Aorta
14	chr6:163848800-163878400	Weak transcription	Pancreas	Pancrea
15	chr6:163849200-163859000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:163850000-163858000	Weak transcription	HepG2	liver
17	chr6:163851000-163858600	Weak transcription	HSMM	muscle
18	chr6:163852000-163858000	Weak transcription	Fetal Lung	lung
19	chr6:163852000-163858800	Weak transcription	HSMMtube	muscle
20	chr6:163852000-163859400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:163852000-163859400	Weak transcription	NHEK	skin
22	chr6:163852000-163880000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:163852200-163858000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:163852200-163858600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:163852200-163858600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:163852200-163865200	Weak transcription	A549	lung
27	chr6:163852200-163875600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:163852200-163875600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:163852600-163858000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:163853000-163858000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:163853200-163858000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:163853200-163858000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:163853200-163858000	Weak transcription	NHDF-Ad	bronchial
34	chr6:163853400-163858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:163853400-163858800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:163853600-163862600	Weak transcription	Esophagus	oesophagus
37	chr6:163853800-163859000	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:163854200-163858000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:163854400-163858600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:163855200-163860000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:163855400-163858000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:163855400-163858400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:163855400-163859600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:163855400-163860000	Weak transcription	Left Ventricle	heart
45	chr6:163855400-163860600	Weak transcription	Psoas Muscle	Psoas
46	chr6:163856200-163858000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:163856200-163858400	Enhancers	Primary B cells from cord blood	blood
48	chr6:163856400-163858000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:163856400-163858600	Weak transcription	Stomach Mucosa	stomach
50	chr6:163856400-163861400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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