Variant report

Variant	rs1216890
Chromosome Location	chr1:113738848-113738849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113737599..113739431-chr1:113933048..113934641,2	MCF-7	breast:
2	chr1:113736472..113740505-chr1:113740581..113744406,4	MCF-7	breast:
3	chr1:113736589..113741335-chr1:113931781..113934442,4	MCF-7	breast:
4	chr1:113733582..113735336-chr1:113738656..113740345,2	K562	blood:
5	chr1:113738414..113740068-chr1:113740785..113743082,3	K562	blood:
6	chr1:113737370..113741159-chr1:113741484..113744250,4	K562	blood:
7	chr1:113737275..113741073-chr1:113748571..113751265,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236887	Chromatin interaction
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10442680	0.86[EUR][1000 genomes]
rs10494152	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10494153	0.86[EUR][1000 genomes]
rs10776764	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1133524	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123070	0.84[EUR][1000 genomes]
rs12123194	0.84[EUR][1000 genomes]
rs12123876	0.84[EUR][1000 genomes]
rs12125209	0.88[CEU][hapmap]
rs12125281	0.84[EUR][1000 genomes]
rs12125282	0.84[EUR][1000 genomes]
rs12126040	0.84[EUR][1000 genomes]
rs12126180	0.84[EUR][1000 genomes]
rs12126412	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12126415	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12127119	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12127186	0.84[EUR][1000 genomes]
rs12129741	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12129773	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12130787	0.84[EUR][1000 genomes]
rs12131406	0.81[EUR][1000 genomes]
rs12132547	0.84[EUR][1000 genomes]
rs12133159	0.81[EUR][1000 genomes]
rs12134261	0.84[EUR][1000 genomes]
rs12134347	0.82[EUR][1000 genomes]
rs12136369	0.84[EUR][1000 genomes]
rs12137440	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12140812	0.86[EUR][1000 genomes]
rs1216791	0.91[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs1216796	0.91[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs1216872	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1216873	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1216878	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216879	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216880	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216881	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216882	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1216884	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1216885	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1216886	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1216889	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216899	0.82[TSI][hapmap]
rs12404563	0.91[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs12405087	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12728957	0.84[EUR][1000 genomes]
rs12736831	0.84[EUR][1000 genomes]
rs1324893	0.86[EUR][1000 genomes]
rs17497065	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1933660	0.84[EUR][1000 genomes]
rs1999905	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1999906	1.00[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs34441710	0.84[EUR][1000 genomes]
rs35021265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35368423	0.84[EUR][1000 genomes]
rs35470019	0.84[EUR][1000 genomes]
rs35495745	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35545085	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35822819	0.81[EUR][1000 genomes]
rs36049267	0.83[AMR][1000 genomes]
rs4427400	0.81[AMR][1000 genomes]
rs4839293	0.80[AMR][1000 genomes]
rs4839296	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs4839297	1.00[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6537773	0.91[CEU][hapmap]
rs6537777	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6683099	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs67028986	0.84[EUR][1000 genomes]
rs67038449	0.84[EUR][1000 genomes]
rs7513596	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7513698	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7542423	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7556534	0.81[EUR][1000 genomes]
rs946219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs946220	0.81[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	nsv2465	chr1:113731589-113776605	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1216890	GNAI3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113733400-113745200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:113734200-113740800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:113734800-113741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:113735000-113742400	Weak transcription	K562	blood
5	chr1:113736200-113741000	Weak transcription	Lung	lung
6	chr1:113738000-113741800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:113738200-113739800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:113738600-113739000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:113738600-113740000	Enhancers	Esophagus	oesophagus
10	chr1:113738800-113741200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:113738800-113742400	Weak transcription	Fetal Intestine Small	intestine
12	chr1:113738800-113742600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:113738800-113745400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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