Variant report

Variant	rs2644142
Chromosome Location	chr1:227721085-227721086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227718832..227721414-chr1:227723108..227725782,2	K562	blood:
2	chr1:227699513..227702199-chr1:227720616..227723558,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10159323	1.00[ASW][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[AMR][1000 genomes]
rs10916168	0.82[ASW][hapmap];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]
rs2814062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2814063	1.00[AFR][1000 genomes]
rs2814065	0.93[LWK][hapmap]
rs2819495	1.00[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	1.00[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	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976960	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:8 , 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	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
4	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
5	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
6	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
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv945338	chr1:227712483-227722545	ZNF genes & repeats Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2644142	NLGN4X	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227714200-227721800	ZNF genes & repeats	Liver	Liver
2	chr1:227715600-227721600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:227718600-227723200	Weak transcription	Psoas Muscle	Psoas
4	chr1:227719800-227721200	ZNF genes & repeats	Aorta	Aorta
5	chr1:227720000-227722000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:227720200-227721200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:227720600-227721200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:227720800-227725800	Weak transcription	Pancreas	Pancrea
9	chr1:227720800-227729200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:227720800-227729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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