Variant report

Variant	rs4522884
Chromosome Location	chr4:122663286-122663287
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10001422	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10011665	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10470915	0.90[EUR][1000 genomes]
rs10471016	0.90[EUR][1000 genomes]
rs11930525	0.90[EUR][1000 genomes]
rs11937861	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1574283	0.90[EUR][1000 genomes]
rs17051397	0.97[EUR][1000 genomes]
rs17051398	1.00[EUR][1000 genomes]
rs1803183	1.00[CHD][hapmap]
rs2621219	0.87[EUR][1000 genomes]
rs2706784	0.85[EUR][1000 genomes]
rs2706786	0.87[EUR][1000 genomes]
rs28515183	0.90[EUR][1000 genomes]
rs28676474	0.90[EUR][1000 genomes]
rs3217767	0.83[CHD][hapmap]
rs3903026	0.90[EUR][1000 genomes]
rs4075713	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs4309856	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4508913	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4571354	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57312551	0.86[EUR][1000 genomes]
rs58127039	0.88[EUR][1000 genomes]
rs59796939	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6825926	1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs6836544	1.00[CHD][hapmap]
rs72913994	0.90[EUR][1000 genomes]
rs7661218	0.86[TSI][hapmap]
rs769243	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv461635	chr4:122633535-122720999	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv595357	chr4:122633535-122720999	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	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
rs4522884	SMCHD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122661400-122664400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr4:122661400-122665400	Enhancers	Fetal Heart	heart
3	chr4:122662000-122664400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:122662000-122664400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:122662200-122664200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:122662200-122664400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:122662400-122663400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:122662600-122663400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr4:122662600-122663400	Enhancers	Fetal Brain Female	brain
10	chr4:122662600-122663600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:122662600-122664000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:122662800-122664200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:122663000-122663400	Enhancers	Fetal Brain Male	brain
14	chr4:122663000-122668800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:122663200-122663400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:122663200-122663400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:122663200-122664400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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