Variant report

Variant	rs878129
Chromosome Location	chr1:114459195-114459196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114443984..114446601-chr1:114458455..114460185,2	K562	blood:
2	chr1:114300624..114304255-chr1:114455595..114460440,4	K562	blood:
3	chr1:114453526..114463040-chr1:114468902..114474133,15	K562	blood:

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10108	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs10494162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494163	0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11102703	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102706	0.88[ASN][1000 genomes]
rs11102707	0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs11102708	0.87[ASN][1000 genomes]
rs11102709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12060750	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12127377	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12129050	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1217444	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503832	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs1553449	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553450	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17852555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1910485	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs1985435	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985436	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41302825	0.86[ASN][1000 genomes]
rs6537800	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669370	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs6674384	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7519860	0.83[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7546851	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756493	0.85[EUR][1000 genomes];0.86[ASN][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs878129	DCLRE1B	cis	normal skin	skin_eQTL
rs878129	DCLRE1B	cis	uninvolved skin	skin_eQTL
rs878129	hCT1828292.1	cis	multi-tissue	Pritchard
rs878129	DCLRE1B	cis	Liver	GTEx
rs878129	DCLRE1B	cis	lesional skin	skin_eQTL
rs878129	DENND2C	cis	cerebellum	SCAN
rs878129	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs878129	ENSG00000118655	cis	multi-tissue	Pritchard
rs878129	DCLRE1B	cis	lymphoblastoid	seeQTL
rs878129	PTPN22	cis	parietal	SCAN
rs878129	DCLRE1B	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114448600-114461400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:114449200-114461800	Weak transcription	Fetal Brain Male	brain
3	chr1:114449800-114470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:114454600-114461000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:114455000-114459800	Weak transcription	HMEC	breast
6	chr1:114455000-114460000	Weak transcription	NHEK	skin
7	chr1:114455200-114459400	Weak transcription	Placenta	Placenta
8	chr1:114455400-114460200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:114455600-114461800	Weak transcription	NH-A	brain
10	chr1:114455800-114459600	Weak transcription	Brain Germinal Matrix	brain
11	chr1:114455800-114465400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:114456000-114459200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:114456000-114459400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:114456000-114460400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:114456000-114460600	Weak transcription	Aorta	Aorta
16	chr1:114456000-114460600	Weak transcription	Fetal Lung	lung
17	chr1:114456000-114462200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:114456000-114462800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:114456000-114463600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:114456200-114459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:114456200-114459200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:114456200-114459200	Weak transcription	Osteobl	bone
23	chr1:114456200-114460000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:114456200-114460200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:114456200-114460600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:114456200-114460600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:114456200-114460800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:114456200-114460800	Weak transcription	Dnd41	blood
29	chr1:114456200-114461200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:114456200-114461200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:114456200-114465400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:114456200-114470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:114456200-114470600	Weak transcription	Brain Substantia Nigra	brain
34	chr1:114456200-114471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:114456400-114459200	Weak transcription	Hela-S3	cervix
36	chr1:114456400-114460200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:114456400-114460200	Weak transcription	NHLF	lung
38	chr1:114456400-114460800	Weak transcription	HSMMtube	muscle
39	chr1:114456400-114470400	Weak transcription	HSMM	muscle
40	chr1:114456600-114459600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:114457200-114459400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:114457200-114459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:114457200-114470600	Weak transcription	Primary T cells from cord blood	blood
44	chr1:114457600-114460800	Weak transcription	Thymus	Thymus
45	chr1:114457600-114461600	Weak transcription	Fetal Stomach	stomach
46	chr1:114457600-114470400	Weak transcription	Fetal Thymus	thymus
47	chr1:114457800-114461600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:114458000-114459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:114458200-114459400	Genic enhancers	K562	blood
50	chr1:114458200-114461600	Weak transcription	Fetal Muscle Leg	muscle

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