Variant report

Variant	rs1216766
Chromosome Location	chr1:113597564-113597565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11102562	0.84[GIH][hapmap]
rs11102573	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11102574	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11102575	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11102576	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11102577	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102578	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102579	0.95[ASN][1000 genomes]
rs11102582	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11584099	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584535	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588345	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590170	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590174	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12028967	0.87[GIH][hapmap]
rs12129863	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12140104	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216760	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1216762	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1216763	0.95[ASN][1000 genomes]
rs1216772	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1216773	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1216775	0.87[EUR][1000 genomes]
rs1216779	0.83[EUR][1000 genomes]
rs1216780	0.88[ASN][1000 genomes]
rs1216781	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[ASN][1000 genomes]
rs1216783	0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1216784	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1216785	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1216790	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1216801	0.80[ASN][1000 genomes]
rs12184285	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12354228	0.84[EUR][1000 genomes]
rs12744009	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12745675	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12746771	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12758163	0.86[ASN][1000 genomes]
rs1419136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544227	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1626085	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17014850	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17030901	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17030905	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17030974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1728218	0.94[JPT][hapmap]
rs1728230	0.96[ASN][1000 genomes]
rs1728238	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1766862	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs1766866	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1778015	0.95[ASN][1000 genomes]
rs1778024	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs1778025	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs1778027	0.80[ASN][1000 genomes]
rs1778028	0.89[ASN][1000 genomes]
rs1983929	0.94[JPT][hapmap]
rs2798686	0.96[ASN][1000 genomes]
rs2798687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798689	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798691	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2798692	0.84[EUR][1000 genomes]
rs2950632	0.85[EUR][1000 genomes]
rs34233065	0.83[EUR][1000 genomes]
rs3889656	0.95[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3951437	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4025965	0.93[ASN][1000 genomes]
rs4301628	0.87[GIH][hapmap]
rs4838975	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4839273	0.87[GIH][hapmap]
rs55894203	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61818171	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61818172	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61818173	0.87[EUR][1000 genomes]
rs61818174	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61818176	0.82[AMR][1000 genomes]
rs6656041	0.83[EUR][1000 genomes]
rs6656311	0.92[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs72683488	0.95[ASN][1000 genomes]
rs773440	0.82[EUR][1000 genomes]
rs9429508	0.88[EUR][1000 genomes]
rs9429509	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429713	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9787311	0.91[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv508537	chr1:113590343-113635803	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1216766	LRIG2	cis	parietal	SCAN
rs1216766	SLC6A17	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113585600-113599200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:113585600-113601800	Weak transcription	Fetal Stomach	stomach
3	chr1:113586600-113599600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113587400-113599600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:113590000-113601400	Weak transcription	Right Atrium	heart
6	chr1:113595600-113597600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:113596200-113597600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:113596200-113597600	Enhancers	Fetal Intestine Large	intestine
9	chr1:113596200-113597600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:113596400-113597800	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:113596600-113597600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:113596600-113599200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:113596600-113599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:113596600-113599600	Weak transcription	Colonic Mucosa	Colon
15	chr1:113596600-113601400	Weak transcription	K562	blood
16	chr1:113596800-113599600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:113596800-113599600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:113596800-113599600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:113596800-113601800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:113596800-113601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:113596800-113601800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:113597000-113597600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr1:113597200-113598600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:113597200-113599200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:113597200-113599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:113597200-113599600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:113597200-113599600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:113597200-113599600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:113597200-113599600	Weak transcription	Fetal Lung	lung
30	chr1:113597200-113599800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:113597200-113599800	Weak transcription	Fetal Kidney	kidney
32	chr1:113597200-113599800	Weak transcription	HepG2	liver
33	chr1:113597400-113599200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:113597400-113599400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:113597400-113599600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:113597400-113599600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:113597400-113599800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:113597400-113601600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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