Variant report

Variant	rs1778015
Chromosome Location	chr1:113602406-113602407
allele	C/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: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11102575	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs11102576	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs11102577	0.87[ASN][1000 genomes]
rs11102578	0.94[ASN][1000 genomes]
rs11102579	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102581	0.92[EUR][1000 genomes]
rs11102582	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12140104	0.95[ASN][1000 genomes]
rs1216760	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216762	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216763	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216766	0.95[ASN][1000 genomes]
rs1216768	0.90[EUR][1000 genomes]
rs1216772	0.94[JPT][hapmap]
rs1216780	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1216781	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1216783	0.94[JPT][hapmap]
rs1216790	0.87[ASN][1000 genomes]
rs1216801	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1216804	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12184285	0.94[JPT][hapmap]
rs12568813	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12744009	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12746771	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs12758163	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1419136	0.95[ASN][1000 genomes]
rs1544227	0.94[JPT][hapmap]
rs1619133	0.91[EUR][1000 genomes]
rs1626085	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17030905	0.81[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs17030974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1728218	0.94[JPT][hapmap]
rs1728230	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1728238	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1766862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1766863	0.92[EUR][1000 genomes]
rs1766866	0.83[ASN][1000 genomes]
rs1778018	0.92[EUR][1000 genomes]
rs1778024	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1778025	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1778027	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1778028	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983929	0.94[JPT][hapmap]
rs2485964	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2798686	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798687	0.95[ASN][1000 genomes]
rs2798689	0.95[ASN][1000 genomes]
rs2840294	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3889656	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs3951437	0.87[ASN][1000 genomes]
rs4025965	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838975	0.95[ASN][1000 genomes]
rs55894203	0.90[ASN][1000 genomes]
rs6656311	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs72683488	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429509	0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1778015	KCNA10	cis	parietal	SCAN
rs1778015	GPR3	trans	parietal	SCAN
rs1778015	LOC149620	cis	cerebellum	SCAN
rs1778015	LRIG2	cis	parietal	SCAN
rs1778015	SLC6A17	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113599000-113603000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:113600400-113614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:113600400-113614800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:113600400-113615000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113600600-113606800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:113601000-113602600	Enhancers	HUVEC	blood vessel
7	chr1:113601000-113602800	Enhancers	HepG2	liver
8	chr1:113601200-113602600	Enhancers	Fetal Intestine Small	intestine
9	chr1:113601400-113602600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:113601400-113602600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:113601400-113602600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:113601400-113602600	Enhancers	Spleen	Spleen
13	chr1:113601400-113602600	Enhancers	K562	blood
14	chr1:113601400-113602800	Enhancers	Fetal Heart	heart
15	chr1:113601400-113603000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:113601600-113602600	Enhancers	Fetal Intestine Large	intestine
17	chr1:113601600-113602600	Enhancers	Placenta	Placenta
18	chr1:113601600-113602800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:113601800-113602600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:113601800-113602600	Enhancers	Fetal Brain Female	brain
21	chr1:113602400-113606800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:113602400-113615000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links