Variant report

Variant	rs2819495
Chromosome Location	chr1:227735257-227735258
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227733749..227736446-chr1:227749685..227751475,2	K562	blood:
2	chr1:227733965..227736657-chr1:227743143..227745274,2	K562	blood:
3	chr1:227729010..227735281-chr1:227748522..227752811,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction
ENSG00000202264	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10159323	1.00[ASW][hapmap];0.93[LWK][hapmap]
rs10916168	0.82[ASW][hapmap];0.93[LWK][hapmap];0.80[AFR][1000 genomes]
rs1817929	1.00[AFR][1000 genomes]
rs2029838	0.92[LWK][hapmap]
rs2453681	0.93[LWK][hapmap];0.84[AFR][1000 genomes]
rs2492633	0.95[AFR][1000 genomes]
rs2644142	1.00[AFR][1000 genomes]
rs2814062	1.00[AFR][1000 genomes]
rs2814063	1.00[AFR][1000 genomes]
rs2814065	0.93[LWK][hapmap]
rs2819497	1.00[AFR][1000 genomes]
rs2819504	0.86[LWK][hapmap];0.84[AFR][1000 genomes]
rs2819505	0.93[LWK][hapmap];0.86[MKK][hapmap]
rs2819523	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2935148	1.00[ASW][hapmap];0.93[LWK][hapmap]
rs41307664	1.00[EUR][1000 genomes]
rs6426466	0.83[AFR][1000 genomes]
rs6689469	0.83[AMR][1000 genomes]
rs7514748	1.00[EUR][1000 genomes]
rs903689	0.82[AFR][1000 genomes]
rs903696	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs976960	0.82[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2819495	NLGN4X	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227730800-227736000	Enhancers	Fetal Muscle Trunk	muscle
2	chr1:227730800-227736000	Enhancers	Fetal Muscle Leg	muscle
3	chr1:227730800-227736000	Enhancers	Pancreas	Pancrea
4	chr1:227731000-227735400	Weak transcription	Colonic Mucosa	Colon
5	chr1:227731000-227748400	Weak transcription	Right Atrium	heart
6	chr1:227731200-227735800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:227731200-227739000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:227731600-227736400	Weak transcription	Gastric	stomach
9	chr1:227734600-227738600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:227734800-227735800	Weak transcription	Placenta	Placenta
11	chr1:227734800-227735800	Flanking Active TSS	HepG2	liver
12	chr1:227735000-227736200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:227735200-227737000	Enhancers	Rectal Mucosa Donor 29	rectum

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