Variant report

Variant	rs1230319
Chromosome Location	chr6:163898797-163898798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163896082..163898816-chr6:163902076..163903998,2	K562	blood:
2	chr6:163855274..163857032-chr6:163897787..163900423,2	K562	blood:
3	chr6:163892454..163895409-chr6:163896616..163898931,2	K562	blood:
4	chr6:163896776..163899468-chr6:163904713..163906625,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACRG-3	chr6:163898510-163899785	NONHSAT115964

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12194670	1.00[AFR][1000 genomes]
rs12199141	1.00[AFR][1000 genomes]
rs12199664	1.00[AFR][1000 genomes]
rs1737605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2321699	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2759397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2784868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163878800-163910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
3	chr6:163880600-163906600	Weak transcription	Gastric	stomach
4	chr6:163881800-163901000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:163882000-163899800	Weak transcription	Placenta	Placenta
7	chr6:163882000-163900000	Weak transcription	Fetal Thymus	thymus
8	chr6:163882000-163906600	Weak transcription	Thymus	Thymus
9	chr6:163883000-163900800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:163883000-163900800	Weak transcription	NH-A	brain
11	chr6:163883000-163906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:163887200-163900000	Weak transcription	Fetal Stomach	stomach
13	chr6:163888400-163902800	Weak transcription	Right Atrium	heart
14	chr6:163888400-163908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:163890000-163900200	Weak transcription	Liver	Liver
16	chr6:163890000-163906200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:163890800-163911400	Weak transcription	Osteobl	bone
18	chr6:163891400-163900000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:163891400-163900000	Weak transcription	Lung	lung
20	chr6:163891400-163906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:163891400-163910200	Weak transcription	HUVEC	blood vessel
22	chr6:163891600-163900200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:163891600-163905000	Weak transcription	K562	blood
24	chr6:163891800-163899400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:163891800-163902000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:163892000-163904200	Weak transcription	NHDF-Ad	bronchial
27	chr6:163892200-163899200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:163892200-163899800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:163892200-163911400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:163892400-163899800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:163892400-163899800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:163892400-163903400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:163892600-163899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:163892600-163906600	Weak transcription	NHEK	skin
35	chr6:163892600-163910400	Weak transcription	HMEC	breast
36	chr6:163892800-163900200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:163892800-163900400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:163893000-163899600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:163893000-163912800	Weak transcription	Fetal Brain Male	brain
40	chr6:163893200-163899400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:163893200-163899400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:163893400-163899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:163893400-163900000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:163893400-163900000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:163893400-163912000	Weak transcription	Fetal Lung	lung
46	chr6:163893600-163899400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:163893600-163899400	Weak transcription	HepG2	liver
48	chr6:163893600-163899800	Weak transcription	HSMM	muscle
49	chr6:163893600-163901200	Weak transcription	Fetal Kidney	kidney
50	chr6:163893600-163904600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links