Variant report

Variant	rs34515259
Chromosome Location	chr1:212462778-212462779
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212317380..212319977-chr1:212460933..212463499,2	K562	blood:
2	chr1:212348711..212350970-chr1:212462639..212464212,2	K562	blood:
3	chr1:212325528..212328341-chr1:212462025..212464406,2	K562	blood:
4	chr1:212216853..212219063-chr1:212462611..212464754,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10494951	0.84[AMR][1000 genomes]
rs10863960	0.81[EUR][1000 genomes]
rs10863961	0.84[EUR][1000 genomes]
rs11585215	0.86[EUR][1000 genomes]
rs12740519	0.85[EUR][1000 genomes]
rs12743785	0.82[EUR][1000 genomes]
rs12746203	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2358448	0.84[EUR][1000 genomes]
rs34447409	0.82[EUR][1000 genomes]
rs34836421	0.85[EUR][1000 genomes]
rs35556190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35822123	0.88[EUR][1000 genomes]
rs4540733	0.83[EUR][1000 genomes]
rs55814152	0.86[EUR][1000 genomes]
rs6661987	0.85[EUR][1000 genomes]
rs6667199	0.86[EUR][1000 genomes]
rs6676208	0.83[EUR][1000 genomes]
rs6693849	0.89[EUR][1000 genomes]
rs71646142	0.81[EUR][1000 genomes]
rs71646143	0.81[EUR][1000 genomes]
rs71646153	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71646158	0.88[EUR][1000 genomes]
rs71646159	0.83[EUR][1000 genomes]
rs7546833	0.82[EUR][1000 genomes]
rs968531	0.86[EUR][1000 genomes]
rs968532	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34515259	RP11-15I11.3	cis	Thyroid	GTEx
rs34515259	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs34515259	RP11-15I11.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212457400-212463400	Active TSS	Right Ventricle	heart
2	chr1:212457600-212462800	Active TSS	Psoas Muscle	Psoas
3	chr1:212458000-212463400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:212459800-212462800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:212459800-212463000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:212459800-212463000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr1:212460000-212463800	Active TSS	Right Atrium	heart
8	chr1:212460200-212462800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr1:212460200-212462800	Flanking Active TSS	Dnd41	blood
10	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
11	chr1:212460400-212463000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr1:212460800-212464400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212461000-212462800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:212461000-212463000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:212461000-212464400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:212461000-212464600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:212461000-212464600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:212461000-212464600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:212461000-212464800	Weak transcription	Placenta	Placenta
20	chr1:212461000-212466000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:212461000-212469000	Enhancers	Brain Substantia Nigra	brain
22	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:212461200-212466600	Enhancers	NHEK	skin
24	chr1:212461200-212467200	Enhancers	HMEC	breast
25	chr1:212461400-212462800	Flanking Active TSS	Liver	Liver
26	chr1:212461400-212463000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr1:212461400-212464400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr1:212461600-212463400	Transcr. at gene 5' and 3'	K562	blood
29	chr1:212461600-212463600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:212461600-212463600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:212461600-212463800	Enhancers	Small Intestine	intestine
32	chr1:212461600-212464400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:212461600-212465400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:212461600-212465600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr1:212461600-212468800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:212461800-212462800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:212461800-212463400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:212461800-212463600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:212461800-212463600	Active TSS	Stomach Smooth Muscle	stomach
40	chr1:212461800-212463800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:212461800-212464400	Weak transcription	Esophagus	oesophagus
42	chr1:212461800-212464400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:212461800-212464400	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:212461800-212464400	Weak transcription	Fetal Thymus	thymus
45	chr1:212461800-212464400	Weak transcription	Gastric	stomach
46	chr1:212461800-212464400	Weak transcription	Lung	lung
47	chr1:212461800-212464400	Weak transcription	Pancreas	Pancrea
48	chr1:212461800-212464600	Weak transcription	Colonic Mucosa	Colon
49	chr1:212461800-212464800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:212461800-212465000	Enhancers	NHLF	lung

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