Variant report

Variant	rs6758434
Chromosome Location	chr2:51900836-51900837
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11563268	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694738	0.89[EUR][1000 genomes]
rs12105026	0.95[ASN][1000 genomes]
rs1400101	0.85[ASN][1000 genomes]
rs1400103	0.95[EUR][1000 genomes]
rs1400104	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400105	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1516177	0.95[ASN][1000 genomes]
rs1516178	0.86[EUR][1000 genomes]
rs1516181	0.95[EUR][1000 genomes]
rs1516182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1516198	0.84[ASN][1000 genomes]
rs1878136	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2354980	0.84[EUR][1000 genomes]
rs2883570	0.84[EUR][1000 genomes]
rs2883571	0.91[ASN][1000 genomes]
rs4971756	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6739137	0.93[ASN][1000 genomes]
rs966733	0.86[EUR][1000 genomes]
rs966734	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv874069	chr2:51723107-52006583	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011738	chr2:51731251-51976068	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv581887	chr2:51883456-51927714	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv874072	chr2:51883456-51928042	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv581888	chr2:51900836-51927714	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6758434	KLRAQ1	cis	parietal	SCAN
rs6758434	JARID2	trans	lymphoblastoid	seeQTL
rs6758434	CCDC104	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:51900000-51902200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:51900400-51901400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr2:51900400-51901400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:51900600-51901000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr2:51900600-51901000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:51900600-51901200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:51900600-51901200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:51900600-51901200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:51900800-51901200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:51900800-51901200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:51900800-51901200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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