Variant report

Variant	rs12453682
Chromosome Location	chr17:37770005-37770006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37769395..37771553-chr17:37883791..37886141,2	K562	blood:
2	chr17:37768363..37771309-chr17:37772118..37774468,3	K562	blood:
3	chr17:37769144..37771005-chr17:37773634..37775729,2	MCF-7	breast:
4	chr17:37763061..37765644-chr17:37767093..37771195,3	K562	blood:
5	chr17:37763559..37766796-chr17:37767970..37771104,4	K562	blood:
6	chr17:37769208..37773729-chr17:37777189..37781252,6	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEUROD2-2	chr17:37769986-37770227	NONHSAT053460

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000171532	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1053651	0.85[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10852934	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11651497	0.90[ASN][1000 genomes]
rs11658678	0.81[CEU][hapmap]
rs11869286	0.87[GIH][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs12150298	0.85[TSI][hapmap]
rs12150603	0.82[TSI][hapmap];0.82[YRI][hapmap]
rs12940986	0.85[TSI][hapmap];0.91[YRI][hapmap]
rs14050	0.82[TSI][hapmap]
rs1476278	0.85[TSI][hapmap]
rs1495099	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1874228	0.87[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1877031	0.81[ASW][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2247862	0.82[TSI][hapmap]
rs2271308	0.86[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2271309	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2517955	0.82[TSI][hapmap];0.91[YRI][hapmap]
rs2517957	0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs2517958	0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs2941503	0.82[TSI][hapmap]
rs2941504	0.82[TSI][hapmap]
rs2952151	0.82[TSI][hapmap]
rs33953566	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3751903	0.89[ASN][1000 genomes]
rs3764352	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.90[ASN][1000 genomes]
rs3764353	0.90[ASN][1000 genomes]
rs3794712	0.87[ASN][1000 genomes]
rs3817160	0.89[ASN][1000 genomes]
rs4794817	0.89[ASN][1000 genomes]
rs4795388	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4795389	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795390	0.89[ASN][1000 genomes]
rs879606	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs881844	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs903502	0.90[TSI][hapmap]
rs907087	0.82[TSI][hapmap]
rs907089	0.85[TSI][hapmap]
rs907094	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.90[ASN][1000 genomes]
rs9303274	0.85[TSI][hapmap]
rs931992	0.81[ASW][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap]
rs9675194	0.85[TSI][hapmap]
rs9915323	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972882	0.85[TSI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
5	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
12	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
13	nsv908208	chr17:37749259-37781849	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv908209	chr17:37749259-37790340	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv908210	chr17:37761202-37781849	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv908211	chr17:37765047-37782410	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv908212	chr17:37765047-37790340	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12453682	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs12453682	PGAP3	cis	Heart Left Ventricle	GTEx
rs12453682	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37763600-37773600	Weak transcription	Gastric	stomach
2	chr17:37765600-37770400	Enhancers	Fetal Brain Male	brain
3	chr17:37767800-37770200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:37767800-37771800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:37768000-37773600	Weak transcription	Right Atrium	heart
6	chr17:37769200-37771400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:37769800-37770800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:37769800-37771800	Weak transcription	Fetal Brain Female	brain
9	chr17:37770000-37770200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
10	chr17:37770000-37770200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr17:37770000-37770200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links