Variant report

Variant	rs976960
Chromosome Location	chr1:227706046-227706047
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227705164..227707099-chr1:227922346..227924920,2	MCF-7	breast:
2	chr1:227696113..227699015-chr1:227705081..227707461,4	K562	blood:
3	chr1:227704941..227707226-chr1:227710980..227713652,2	K562	blood:
4	chr1:227696655..227700997-chr1:227705079..227707461,4	K562	blood:
5	chr1:227700137..227701945-chr1:227703714..227706435,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10159323	0.82[ASW][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[AMR][1000 genomes]
rs10916168	0.93[LWK][hapmap];0.93[MKK][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1390402	1.00[AMR][1000 genomes]
rs1817929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1826774	1.00[AMR][1000 genomes]
rs1874372	1.00[AMR][1000 genomes]
rs2029838	0.92[LWK][hapmap]
rs2313246	1.00[AMR][1000 genomes]
rs2453681	0.93[LWK][hapmap];0.93[MKK][hapmap];0.84[AFR][1000 genomes]
rs2492633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2644142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2814062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2814063	1.00[AFR][1000 genomes]
rs2814065	0.93[LWK][hapmap]
rs2819495	0.82[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2819497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2819504	0.86[LWK][hapmap];0.84[AFR][1000 genomes]
rs2819505	0.93[LWK][hapmap];1.00[MKK][hapmap]
rs2935148	0.82[ASW][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];1.00[AMR][1000 genomes]
rs2935151	1.00[AMR][1000 genomes]
rs2999738	1.00[AMR][1000 genomes]
rs2999747	1.00[AMR][1000 genomes]
rs3010184	1.00[AMR][1000 genomes]
rs4653513	1.00[AMR][1000 genomes]
rs6426466	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6426467	1.00[AMR][1000 genomes]
rs6662898	1.00[AMR][1000 genomes]
rs7521659	1.00[AMR][1000 genomes]
rs7540705	1.00[AMR][1000 genomes]
rs903689	0.82[AFR][1000 genomes]
rs903696	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9943170	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv945337	chr1:227680551-227712483	ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs976960	NLGN4X	trans	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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