Variant report

Variant	rs2530685
Chromosome Location	chr22:30106659-30106660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11090572	0.88[AFR][1000 genomes]
rs2158619	0.95[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245194	0.84[EUR][1000 genomes]
rs2348686	0.86[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs2527334	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2527335	0.86[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2530662	0.86[CEU][hapmap]
rs2857631	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857633	0.82[ASW][hapmap]
rs2857638	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2857643	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2857646	0.84[EUR][1000 genomes]
rs2857647	0.86[EUR][1000 genomes]
rs2857652	0.95[CEU][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56246484	0.84[EUR][1000 genomes]
rs5763378	0.86[CEU][hapmap]
rs6519793	0.86[CEU][hapmap]
rs731647	0.95[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs756053	0.95[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8140060	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv914965	chr22:30086144-30112226	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1816879	chr22:30096309-30126906	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv471194	chr22:30103476-30128380	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv471195	chr22:30103476-30128380	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv914967	chr22:30103476-30133579	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2530685	NIPSNAP1	cis	parietal	SCAN
rs2530685	THOC5	cis	cerebellum	SCAN
rs2530685	KIAA1671	cis	cerebellum	SCAN
rs2530685	C22orf30	cis	parietal	SCAN
rs2530685	CRYBB3	cis	parietal	SCAN
rs2530685	C11orf1	trans	parietal	SCAN
rs2530685	PITPNB	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30096400-30107400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr22:30098800-30115600	Weak transcription	Right Atrium	heart
3	chr22:30104600-30108000	Enhancers	Fetal Muscle Leg	muscle
4	chr22:30105800-30108400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:30106000-30107000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr22:30106000-30107400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr22:30106000-30107800	Enhancers	Spleen	Spleen
8	chr22:30106200-30106800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr22:30106200-30107600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:30106200-30107800	Enhancers	HSMMtube	muscle
11	chr22:30106400-30107200	Enhancers	Psoas Muscle	Psoas
12	chr22:30106400-30107400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr22:30106400-30107600	Enhancers	Fetal Brain Male	brain
14	chr22:30106400-30107800	Enhancers	Fetal Brain Female	brain
15	chr22:30106400-30107800	Enhancers	Pancreas	Pancrea
16	chr22:30106600-30106800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr22:30106600-30106800	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr22:30106600-30107000	Bivalent Enhancer	Brain Hippocampus Middle	brain
19	chr22:30106600-30107400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr22:30106600-30107400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
21	chr22:30106600-30107400	Flanking Active TSS	Hela-S3	cervix

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