Variant report

Variant	rs7762052
Chromosome Location	chr6:37767529-37767530
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37760526..37762581-chr6:37765798..37767816,2	MCF-7	breast:
2	chr6:37758926..37760720-chr6:37767100..37768812,2	K562	blood:
3	chr6:37761965..37764146-chr6:37767297..37769364,2	MCF-7	breast:
4	chr6:37765846..37768187-chr6:37771368..37772947,2	K562	blood:
5	chr6:37764796..37769141-chr6:37786360..37788768,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10428769	0.81[AMR][1000 genomes]
rs10485030	0.83[ASW][hapmap];0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs10947702	0.84[CEU][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs10947704	0.95[CEU][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs11751781	0.84[CEU][hapmap]
rs11752521	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs11752809	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11752814	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11753300	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11755095	0.81[AMR][1000 genomes]
rs11755629	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs11756713	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs11757161	0.81[AMR][1000 genomes]
rs11759458	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11759826	0.84[CEU][hapmap]
rs11964613	0.82[JPT][hapmap]
rs11964671	0.82[JPT][hapmap]
rs11967129	0.81[AMR][1000 genomes]
rs11969988	0.81[AMR][1000 genomes]
rs11970017	0.82[JPT][hapmap]
rs12661378	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs12661702	0.81[AMR][1000 genomes]
rs12662426	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs12664091	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs12664768	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs13190751	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13195545	0.81[AMR][1000 genomes]
rs13198459	0.82[JPT][hapmap]
rs13203867	0.82[JPT][hapmap]
rs13205214	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs13205311	0.81[AMR][1000 genomes]
rs13206035	0.89[CEU][hapmap]
rs13207526	0.82[JPT][hapmap]
rs13210967	0.82[JPT][hapmap]
rs13219500	0.82[JPT][hapmap]
rs16890185	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16890194	0.82[JPT][hapmap]
rs2025431	0.81[AMR][1000 genomes]
rs2103950	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2273441	0.89[CEU][hapmap]
rs2274091	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs2453882	0.82[JPT][hapmap]
rs2645096	0.82[JPT][hapmap]
rs2645098	0.82[JPT][hapmap]
rs2645126	0.82[JPT][hapmap]
rs2645130	0.81[AMR][1000 genomes]
rs2842499	0.82[JPT][hapmap]
rs2842510	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap]
rs2842511	0.82[YRI][hapmap]
rs2842514	0.82[JPT][hapmap]
rs2842516	0.82[JPT][hapmap]
rs2842521	0.87[CEU][hapmap]
rs2842524	0.82[JPT][hapmap]
rs34254045	0.81[AMR][1000 genomes]
rs35122358	0.81[AMR][1000 genomes]
rs35216205	0.81[AMR][1000 genomes]
rs35849984	0.85[AMR][1000 genomes]
rs3844314	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs4394213	0.82[JPT][hapmap]
rs55679841	0.81[AMR][1000 genomes]
rs55996712	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56129320	0.83[AMR][1000 genomes]
rs56177150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58333612	0.81[AMR][1000 genomes]
rs58611435	0.81[AMR][1000 genomes]
rs61411293	0.81[AMR][1000 genomes]
rs6458032	0.95[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs6458037	0.82[JPT][hapmap]
rs6903743	0.81[AMR][1000 genomes]
rs6906289	0.81[AMR][1000 genomes]
rs6908106	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6908761	0.82[JPT][hapmap]
rs6910180	0.85[JPT][hapmap]
rs6910715	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6910837	0.82[JPT][hapmap]
rs6911481	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6911716	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs6916535	0.82[JPT][hapmap]
rs6919884	0.82[JPT][hapmap]
rs6923132	0.82[JPT][hapmap]
rs6923254	0.82[JPT][hapmap]
rs6936260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71569394	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7742226	0.94[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs7746266	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs7748312	0.89[CEU][hapmap]
rs7750445	1.00[JPT][hapmap]
rs7759145	0.81[AMR][1000 genomes]
rs7759792	0.84[CEU][hapmap]
rs7761561	0.95[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs7764130	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs7773419	0.83[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs7775794	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs7776025	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7762052	C6orf129	cis	parietal	SCAN
rs7762052	C6orf222	cis	cerebellum	SCAN
rs7762052	FTSJD2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37759200-37768400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:37759800-37768600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:37766400-37768200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:37766400-37768800	Enhancers	Fetal Stomach	stomach
5	chr6:37766400-37775400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:37766800-37767800	Enhancers	Fetal Intestine Small	intestine
7	chr6:37767000-37767600	Enhancers	Stomach Mucosa	stomach
8	chr6:37767000-37767800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:37767000-37767800	Enhancers	Fetal Intestine Large	intestine
10	chr6:37767200-37767600	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:37767200-37767800	Enhancers	Aorta	Aorta
12	chr6:37767200-37767800	Enhancers	Liver	Liver
13	chr6:37767400-37768800	Enhancers	HepG2	liver
14	chr6:37767400-37775400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:37767400-37777000	Weak transcription	Right Atrium	heart

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