Variant report

Variant	rs2798686
Chromosome Location	chr1:113601445-113601446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113572393..113574061-chr1:113600793..113602856,2	MCF-7	breast:
2	chr1:113590314..113592778-chr1:113600467..113602579,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11102575	0.94[JPT][hapmap]
rs11102576	0.94[JPT][hapmap]
rs11102577	0.86[ASN][1000 genomes]
rs11102578	0.95[ASN][1000 genomes]
rs11102579	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102581	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11102582	0.91[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12140104	0.94[ASN][1000 genomes]
rs1216760	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216762	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216763	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1216766	0.96[ASN][1000 genomes]
rs1216768	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1216772	0.94[JPT][hapmap]
rs1216780	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1216781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1216783	0.94[JPT][hapmap]
rs1216790	0.88[ASN][1000 genomes]
rs1216801	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1216804	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12184285	0.94[JPT][hapmap]
rs12568813	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12744009	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12746771	0.94[JPT][hapmap]
rs12758163	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1419136	0.96[ASN][1000 genomes]
rs1544227	0.94[JPT][hapmap]
rs1619133	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1626085	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17030905	0.94[JPT][hapmap]
rs17030974	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1728218	0.94[JPT][hapmap]
rs1728230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728238	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1766862	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1766863	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1766866	0.84[ASN][1000 genomes]
rs1778015	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778018	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1778024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778027	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1778028	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983929	0.94[JPT][hapmap]
rs2485964	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2798687	0.96[ASN][1000 genomes]
rs2798689	0.94[ASN][1000 genomes]
rs2840294	0.96[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs3889656	0.87[JPT][hapmap]
rs3951437	0.88[ASN][1000 genomes]
rs4025965	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838975	0.94[ASN][1000 genomes]
rs55894203	0.89[ASN][1000 genomes]
rs6656311	0.94[JPT][hapmap]
rs72683488	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429509	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9429713	0.81[ASN][1000 genomes]
rs9787311	0.94[JPT][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2798686	LOC149620	cis	cerebellum	SCAN
rs2798686	LRIG2	cis	parietal	SCAN
rs2798686	KCNA10	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113585600-113601800	Weak transcription	Fetal Stomach	stomach
2	chr1:113596800-113601800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:113596800-113601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113596800-113601800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:113597400-113601600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:113599000-113603000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:113599600-113602200	Enhancers	Fetal Muscle Trunk	muscle
8	chr1:113599800-113601600	Weak transcription	Fetal Intestine Large	intestine
9	chr1:113600200-113601600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:113600200-113601600	Weak transcription	Placenta	Placenta
11	chr1:113600200-113601600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:113600200-113601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:113600400-113601600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:113600400-113601600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:113600400-113601600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:113600400-113601600	Weak transcription	Left Ventricle	heart
17	chr1:113600400-113601600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:113600400-113601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:113600400-113601800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:113600400-113601800	Weak transcription	Colonic Mucosa	Colon
21	chr1:113600400-113614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:113600400-113614800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:113600400-113615000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:113600600-113601600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:113600600-113601600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:113600600-113601800	Weak transcription	Fetal Brain Female	brain
27	chr1:113600600-113606800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:113600800-113602400	Enhancers	Fetal Lung	lung
29	chr1:113601000-113602600	Enhancers	HUVEC	blood vessel
30	chr1:113601000-113602800	Enhancers	HepG2	liver
31	chr1:113601200-113602600	Enhancers	Fetal Intestine Small	intestine
32	chr1:113601400-113601600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:113601400-113601800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:113601400-113602000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:113601400-113602000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:113601400-113602000	Enhancers	Right Ventricle	heart
37	chr1:113601400-113602200	Enhancers	Adipose Nuclei	Adipose
38	chr1:113601400-113602400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:113601400-113602400	Enhancers	Fetal Kidney	kidney
40	chr1:113601400-113602400	Enhancers	Fetal Muscle Leg	muscle
41	chr1:113601400-113602400	Enhancers	Right Atrium	heart
42	chr1:113601400-113602400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:113601400-113602600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:113601400-113602600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:113601400-113602600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:113601400-113602600	Enhancers	Spleen	Spleen
47	chr1:113601400-113602600	Enhancers	K562	blood
48	chr1:113601400-113602800	Enhancers	Fetal Heart	heart
49	chr1:113601400-113603000	Enhancers	Cortex derived primary cultured neurospheres	brain

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