Variant report

Variant	rs6669370
Chromosome Location	chr1:114506675-114506676
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113495708..113498262-chr1:114506476..114508244,2	K562	blood:
2	chr1:114500011..114502130-chr1:114506605..114508705,2	MCF-7	breast:
3	chr1:114506613..114508905-chr1:114518738..114521439,2	MCF-7	breast:
4	chr1:114472262..114473380-chr1:114505771..114506776,3	MCF-7	breast:
5	chr1:114376437..114378781-chr1:114506085..114507975,2	MCF-7	breast:
6	chr1:114500481..114503328-chr1:114506165..114508203,3	MCF-7	breast:
7	chr1:114352766..114354968-chr1:114504894..114507135,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081019	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10108	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494162	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10494163	0.88[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102703	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102706	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102707	0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.89[ASN][1000 genomes]
rs11102708	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102709	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12060750	0.84[ASN][1000 genomes]
rs12125546	0.83[ASN][1000 genomes]
rs12127377	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12129050	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217444	0.86[ASN][1000 genomes]
rs1503832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553449	0.91[ASN][1000 genomes]
rs1553450	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17852555	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1985435	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985436	0.91[ASN][1000 genomes]
rs41302825	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537800	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674384	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7519860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545300	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7546851	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs756493	0.85[ASN][1000 genomes]
rs878129	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]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6669370	DCLRE1B	cis	multi-tissue	Pritchard
rs6669370	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs6669370	DCLRE1B	cis	normal skin	skin_eQTL
rs6669370	DCLRE1B	cis	lymphoblastoid	seeQTL
rs6669370	DENND2C	cis	cerebellum	SCAN
rs6669370	PTPN22	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114479000-114517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114484000-114510400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:114484000-114510400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:114484000-114511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114484400-114510400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:114485000-114510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:114489800-114510400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:114490200-114507200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:114490200-114510800	Weak transcription	A549	lung
10	chr1:114490600-114512000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:114492800-114518600	Strong transcription	Dnd41	blood
12	chr1:114493400-114517600	Strong transcription	Fetal Thymus	thymus
13	chr1:114495400-114507200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:114495400-114517400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:114495600-114508600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:114495800-114516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:114495800-114518200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:114496000-114517000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:114496400-114516000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:114496400-114516400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:114496400-114517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:114496400-114517200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:114496400-114517400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:114496400-114517600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:114496400-114518200	Strong transcription	K562	blood
26	chr1:114496400-114519400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:114496600-114518800	Strong transcription	Primary B cells from cord blood	blood
28	chr1:114496800-114508800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:114497000-114516400	Strong transcription	Fetal Intestine Large	intestine
30	chr1:114497000-114517000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:114497200-114516400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:114497200-114516400	Strong transcription	GM12878-XiMat	blood
33	chr1:114497600-114517600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:114497800-114517400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:114498000-114507800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:114498000-114517400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:114498800-114518200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:114499600-114511200	Weak transcription	Stomach Mucosa	stomach
39	chr1:114500000-114517600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:114500200-114508400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:114500800-114508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:114501000-114510200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:114501800-114508600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:114501800-114516800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:114502000-114507400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:114502000-114508800	Weak transcription	Fetal Brain Male	brain
47	chr1:114502000-114511200	Weak transcription	Fetal Heart	heart
48	chr1:114502200-114508000	Weak transcription	Brain Angular Gyrus	brain
49	chr1:114502200-114510200	Weak transcription	Right Ventricle	heart
50	chr1:114502800-114510400	Weak transcription	Ovary	ovary

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