Variant report

Variant	rs6690942
Chromosome Location	chr1:151629958-151629959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151625892..151628337-chr1:151629163..151630750,2	MCF-7	breast:
2	chr1:151628251..151631523-chr1:151631798..151635161,3	MCF-7	breast:
3	1:151402394-151411623..1:151618750-151636526	GM12878	blood:
4	chr1:151512144..151513669-chr1:151629955..151632572,2	MCF-7	breast:
5	chr1:151629068..151630883-chr1:151630924..151632561,2	MCF-7	breast:
6	1:151171193-151178589..1:151618750-151636526	Hela-S3	cervix:
7	chr1:151626801..151630582-chr1:151633490..151635442,3	MCF-7	breast:
8	1:151592347-151603110..1:151618750-151636526	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000238711	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000232536	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12402668	0.82[AMR][1000 genomes]
rs12733147	0.87[ASN][1000 genomes]
rs12745172	0.86[ASN][1000 genomes]
rs12746897	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12751044	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752221	0.88[ASN][1000 genomes]
rs1607933	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17641780	0.90[JPT][hapmap]
rs2275920	0.81[AMR][1000 genomes]
rs2280473	0.83[ASN][1000 genomes]
rs2280475	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3204344	0.95[JPT][hapmap]
rs35388624	0.88[ASN][1000 genomes]
rs35654949	0.88[ASN][1000 genomes]
rs3828056	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4466658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56130043	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58983661	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59527020	0.82[AMR][1000 genomes]
rs61501378	0.82[AMR][1000 genomes]
rs6676545	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs6685067	0.95[JPT][hapmap]
rs6687866	0.95[JPT][hapmap]
rs6702842	0.95[JPT][hapmap]

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	nsv2843	chr1:151600069-151644709	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6690942	LCE1C	cis	parietal	SCAN
rs6690942	GATAD2B	cis	cerebellum	SCAN
rs6690942	LINGO4	cis	cerebellum	SCAN
rs6690942	BCL9	cis	cerebellum	SCAN
rs6690942	VPS72	cis	cerebellum	SCAN
rs6690942	MTMR11	cis	cerebellum	SCAN
rs6690942	TDRKH	cis	cerebellum	SCAN
rs6690942	NPR1	cis	cerebellum	SCAN
rs6690942	SPRR2G	cis	cerebellum	SCAN
rs6690942	SLC27A3	cis	cerebellum	SCAN
rs6690942	SPRR2B	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151587600-151640600	Weak transcription	Fetal Brain Male	brain
2	chr1:151588200-151665200	Weak transcription	Aorta	Aorta
3	chr1:151591000-151630800	Weak transcription	Fetal Kidney	kidney
4	chr1:151591200-151675400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:151592600-151633800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:151592800-151630600	Weak transcription	Hela-S3	cervix
7	chr1:151594000-151652800	Weak transcription	Right Ventricle	heart
8	chr1:151603000-151663200	Weak transcription	Colonic Mucosa	Colon
9	chr1:151606800-151630800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:151608200-151630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:151610200-151633800	Weak transcription	HUVEC	blood vessel
12	chr1:151610600-151630600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:151610600-151631000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:151610600-151652200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:151610600-151665000	Weak transcription	Lung	lung
16	chr1:151610800-151631000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:151611400-151630400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:151611400-151630400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:151611400-151631000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:151611600-151633000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:151611600-151634200	Weak transcription	Psoas Muscle	Psoas
22	chr1:151611600-151637600	Weak transcription	Fetal Heart	heart
23	chr1:151611600-151639800	Weak transcription	K562	blood
24	chr1:151611600-151640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:151611600-151643800	Weak transcription	Pancreas	Pancrea
26	chr1:151611600-151668200	Weak transcription	Gastric	stomach
27	chr1:151611800-151630400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:151612200-151630800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:151612400-151634600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:151612800-151630400	Weak transcription	HSMMtube	muscle
31	chr1:151612800-151630800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:151612800-151633800	Weak transcription	HSMM	muscle
33	chr1:151612800-151652400	Weak transcription	HMEC	breast
34	chr1:151613800-151630600	Weak transcription	NH-A	brain
35	chr1:151614000-151630600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:151614000-151630600	Weak transcription	NHEK	skin
37	chr1:151618000-151642600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:151618000-151667600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:151619400-151630600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:151620800-151631800	Weak transcription	Left Ventricle	heart
41	chr1:151621400-151632000	Weak transcription	Fetal Lung	lung
42	chr1:151621600-151630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:151622400-151630600	Weak transcription	Fetal Thymus	thymus
44	chr1:151622800-151643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:151623000-151630600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:151623000-151630600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:151623000-151630600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:151623000-151631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:151623000-151641600	Weak transcription	Ovary	ovary
50	chr1:151624000-151632000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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