Variant report

Variant	rs16844824
Chromosome Location	chr2:160989296-160989297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10197183	0.86[YRI][hapmap]
rs10454740	0.80[CEU][hapmap]
rs10497208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929970	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10929971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885142	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11887337	0.80[CEU][hapmap]
rs11895959	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11902965	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476618	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13027372	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13394776	0.80[CEU][hapmap]
rs13413256	0.88[YRI][hapmap]
rs13426637	0.85[YRI][hapmap]
rs13427061	0.81[CEU][hapmap]
rs1457233	0.80[CEU][hapmap]
rs1457235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457236	0.82[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457237	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457238	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457239	0.86[YRI][hapmap]
rs1457240	0.81[CEU][hapmap]
rs1471120	0.81[CEU][hapmap]
rs1471121	0.81[CEU][hapmap]
rs1902622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061288	0.80[CEU][hapmap]
rs2061290	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124971	0.82[YRI][hapmap]
rs2290706	0.82[YRI][hapmap]
rs2357773	0.84[CEU][hapmap]
rs2357861	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2715929	0.80[CEU][hapmap]
rs2884268	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2925763	0.81[CEU][hapmap]
rs34064895	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762905	0.85[EUR][1000 genomes]
rs34955537	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35271738	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35720878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35859214	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755547	0.82[YRI][hapmap]
rs3796103	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233679	0.81[CEU][hapmap]
rs4265965	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324285	0.81[CEU][hapmap]
rs4426486	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4473342	0.86[YRI][hapmap]
rs4580348	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664313	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664315	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4665160	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62177889	0.80[AFR][1000 genomes]
rs6432593	0.81[CEU][hapmap]
rs6432600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432603	0.84[CEU][hapmap]
rs6729540	0.80[CEU][hapmap]
rs6758074	0.86[YRI][hapmap]
rs7422400	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs748427	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7558296	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7558852	0.81[CEU][hapmap]
rs7563574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583743	0.84[CEU][hapmap]
rs7584446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586660	0.86[YRI][hapmap]
rs7596372	0.82[YRI][hapmap]
rs7608267	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897832	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996112	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16844824	CYTIP	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:160959200-161004200	Weak transcription	Gastric	stomach
3	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
4	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:160971000-160993800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:160977600-160989600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:160977600-160989600	Strong transcription	HMEC	breast
9	chr2:160980600-160996400	Weak transcription	HSMMtube	muscle
10	chr2:160982800-160993600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:160983000-160993800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:160983000-160993800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:160983200-161005200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:160983400-160993600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:160983400-160993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:160983600-160993800	Weak transcription	Pancreas	Pancrea
17	chr2:160983600-160994000	Weak transcription	Fetal Stomach	stomach
18	chr2:160985200-160993800	Weak transcription	Fetal Intestine Small	intestine
19	chr2:160985400-160993800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:160986000-160989400	Weak transcription	NHEK	skin
21	chr2:160988600-160989800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:160988800-160993600	Weak transcription	HSMM	muscle
23	chr2:160989000-160993600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:160989000-160993600	Weak transcription	Dnd41	blood
25	chr2:160989200-160989400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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