Variant report

Variant	rs12404563
Chromosome Location	chr1:113689835-113689836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113680385..113687065-chr1:113687067..113690757,6	K562	blood:
2	chr1:113688711..113690505-chr1:113784711..113786902,2	MCF-7	breast:
3	chr1:113683011..113687065-chr1:113687072..113690657,5	K562	blood:
4	chr1:113683696..113687122-chr1:113688209..113690807,4	MCF-7	breast:
5	chr1:113674756..113677220-chr1:113688268..113690973,2	K562	blood:
6	chr1:113616013..113618025-chr1:113688637..113691001,2	MCF-7	breast:
7	chr1:113686049..113694370-chr1:113929775..113935752,18	MCF-7	breast:
8	chr1:113687424..113692442-chr1:113930468..113933577,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10442680	0.82[EUR][1000 genomes]
rs10494148	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs10494149	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10494150	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10494152	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs10494153	0.82[EUR][1000 genomes]
rs10776764	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11102590	0.91[EUR][1000 genomes]
rs11102591	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1133524	0.81[AMR][1000 genomes]
rs12070586	0.93[EUR][1000 genomes]
rs12072108	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12073607	0.93[EUR][1000 genomes]
rs12123070	0.95[EUR][1000 genomes]
rs12123194	0.95[EUR][1000 genomes]
rs12123876	0.95[EUR][1000 genomes]
rs12125209	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12125253	0.89[EUR][1000 genomes]
rs12125281	0.95[EUR][1000 genomes]
rs12125282	0.95[EUR][1000 genomes]
rs12126040	0.95[EUR][1000 genomes]
rs12126180	0.95[EUR][1000 genomes]
rs12126412	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12126415	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12127119	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12127186	0.95[EUR][1000 genomes]
rs12129741	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12129773	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs12129924	0.89[EUR][1000 genomes]
rs12130429	0.89[EUR][1000 genomes]
rs12130787	0.95[EUR][1000 genomes]
rs12131406	0.87[EUR][1000 genomes]
rs12132547	0.95[EUR][1000 genomes]
rs12133159	0.87[EUR][1000 genomes]
rs12133521	0.87[EUR][1000 genomes]
rs12134261	0.95[EUR][1000 genomes]
rs12134347	0.93[EUR][1000 genomes]
rs12136369	0.95[EUR][1000 genomes]
rs12137440	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12140812	0.82[EUR][1000 genomes]
rs12141374	0.89[EUR][1000 genomes]
rs12141890	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1216791	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216796	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216797	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1216872	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1216873	0.90[EUR][1000 genomes]
rs1216880	0.81[AMR][1000 genomes]
rs1216884	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1216885	0.81[AMR][1000 genomes]
rs1216886	0.83[AMR][1000 genomes]
rs1216889	0.80[AMR][1000 genomes]
rs1216890	0.91[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs12405087	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12723657	0.89[EUR][1000 genomes]
rs12728957	0.95[EUR][1000 genomes]
rs12732564	0.88[EUR][1000 genomes]
rs12736831	0.95[EUR][1000 genomes]
rs12745847	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12748429	0.89[EUR][1000 genomes]
rs12757593	0.91[EUR][1000 genomes]
rs12760482	0.89[EUR][1000 genomes]
rs1316767	0.89[EUR][1000 genomes]
rs1324893	0.82[EUR][1000 genomes]
rs1661	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17031099	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17031158	0.89[EUR][1000 genomes]
rs17031160	0.89[EUR][1000 genomes]
rs17497065	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1933656	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1933660	0.95[EUR][1000 genomes]
rs1999905	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs1999906	0.89[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs2185105	0.89[EUR][1000 genomes]
rs2185106	0.89[EUR][1000 genomes]
rs2359709	0.88[EUR][1000 genomes]
rs2359710	0.89[EUR][1000 genomes]
rs2359711	0.89[EUR][1000 genomes]
rs34236373	0.89[EUR][1000 genomes]
rs34441710	0.95[EUR][1000 genomes]
rs35368423	0.95[EUR][1000 genomes]
rs35470019	0.95[EUR][1000 genomes]
rs35737003	0.86[EUR][1000 genomes]
rs35793987	0.93[EUR][1000 genomes]
rs35822819	0.87[EUR][1000 genomes]
rs36049267	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4240536	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4427400	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4630126	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4839290	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4839293	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4839295	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4839296	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4839297	0.91[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs56204018	0.93[EUR][1000 genomes]
rs6537773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6537777	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs6683099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67028986	0.95[EUR][1000 genomes]
rs67038449	0.95[EUR][1000 genomes]
rs72685622	0.93[EUR][1000 genomes]
rs749956	0.89[EUR][1000 genomes]
rs7513596	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs7513698	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs7515810	0.89[EUR][1000 genomes]
rs7521854	0.88[EUR][1000 genomes]
rs7540970	0.89[EUR][1000 genomes]
rs7543653	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs7548091	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs7551138	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs7556148	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7556534	0.87[EUR][1000 genomes]
rs946219	0.89[CEU][hapmap]
rs946220	0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9628702	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12404563	GNAI3	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113669800-113690000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:113684400-113692800	Weak transcription	GM12878-XiMat	blood
3	chr1:113685400-113691600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:113685600-113690000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:113685600-113690200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:113685600-113691600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:113686200-113695600	Weak transcription	Stomach Mucosa	stomach
8	chr1:113688200-113692200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:113688400-113691000	Enhancers	Primary T cells from cord blood	blood
10	chr1:113688400-113691000	Enhancers	Fetal Intestine Large	intestine
11	chr1:113688400-113691000	Enhancers	Fetal Intestine Small	intestine
12	chr1:113688400-113691000	Enhancers	Dnd41	blood
13	chr1:113688600-113690200	Flanking Active TSS	HepG2	liver
14	chr1:113688600-113691000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:113688800-113690000	Enhancers	K562	blood
16	chr1:113688800-113690200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:113688800-113690200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:113688800-113690200	Enhancers	HUVEC	blood vessel
19	chr1:113688800-113690800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:113688800-113690800	Enhancers	Placenta	Placenta
21	chr1:113688800-113690800	Enhancers	Fetal Thymus	thymus
22	chr1:113689000-113690000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:113689000-113690200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:113689000-113690200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:113689000-113690400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:113689000-113690600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:113689000-113690600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:113689000-113690600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:113689000-113691000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:113689200-113690000	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:113689200-113690200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:113689200-113690200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:113689200-113690200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:113689200-113690200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:113689200-113690400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:113689200-113690800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr1:113689400-113690000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:113689400-113690000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:113689400-113690200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:113689400-113690600	Enhancers	Thymus	Thymus
41	chr1:113689400-113690800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:113689400-113691000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:113689600-113690400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:113689800-113690200	Enhancers	Lung	lung
45	chr1:113689800-113690400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:113689800-113690800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:113689800-113691000	Enhancers	Small Intestine	intestine
48	chr1:113689800-113691800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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