Variant report

Variant	rs12902073
Chromosome Location	chr15:52447508-52447509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52446493..52448548-chr15:52449558..52451826,2	MCF-7	breast:
2	chr15:52447415..52450073-chr15:52464203..52465781,2	MCF-7	breast:
3	chr15:52399033..52401663-chr15:52446197..52448357,2	MCF-7	breast:
4	chr15:52431718..52434143-chr15:52447215..52449293,2	MCF-7	breast:
5	chr15:52446218..52447744-chr15:52470239..52472909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11070882	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11856177	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438743	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12440354	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440956	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap]
rs12593939	0.82[AMR][1000 genomes]
rs12594679	0.90[ASN][1000 genomes]
rs12595160	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap]
rs12899343	1.00[CEU][hapmap]
rs12901354	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12901730	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12901891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12903769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904831	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12904889	0.91[ASN][1000 genomes]
rs12905698	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12907835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12908742	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908833	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909161	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12909184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12909880	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910052	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12910398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12912428	0.89[ASN][1000 genomes]
rs12916557	0.89[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap]
rs2398	1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34283892	0.90[ASN][1000 genomes]
rs35709612	0.81[EUR][1000 genomes]
rs35827106	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3794543	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4636859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap]
rs4774608	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4776003	0.86[ASN][1000 genomes]
rs4776007	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4776010	0.81[AMR][1000 genomes]
rs4776011	0.89[AMR][1000 genomes]
rs4776014	0.81[AMR][1000 genomes]
rs62014722	0.81[EUR][1000 genomes]
rs66566761	0.81[AMR][1000 genomes]
rs67163040	0.81[AMR][1000 genomes]
rs67447954	0.81[AMR][1000 genomes]
rs7164508	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs7172037	0.81[AMR][1000 genomes]
rs8034097	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902073	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:52423000-52458200	Weak transcription	Dnd41	blood
3	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
4	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
5	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
8	chr15:52436800-52457200	Weak transcription	GM12878-XiMat	blood
9	chr15:52437200-52456800	Weak transcription	HSMM	muscle
10	chr15:52437400-52454000	Weak transcription	NH-A	brain
11	chr15:52437400-52454400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:52438000-52455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:52439200-52463600	Weak transcription	NHEK	skin
15	chr15:52439600-52454800	Weak transcription	NHDF-Ad	bronchial
16	chr15:52441000-52453800	Weak transcription	NHLF	lung
17	chr15:52441000-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:52442000-52455200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:52442200-52454800	Weak transcription	Fetal Intestine Small	intestine
22	chr15:52442200-52455800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
25	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:52442400-52457200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:52442400-52457200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:52442400-52457800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:52442600-52470400	Weak transcription	HMEC	breast
31	chr15:52442800-52454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:52443400-52455400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:52443600-52453800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:52443800-52451000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:52443800-52451400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:52443800-52451600	Weak transcription	Hela-S3	cervix
38	chr15:52443800-52453600	Weak transcription	Spleen	Spleen
39	chr15:52443800-52455200	Weak transcription	Right Ventricle	heart
40	chr15:52443800-52455400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:52443800-52456000	Weak transcription	Fetal Lung	lung
42	chr15:52443800-52457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:52444000-52448400	Weak transcription	Liver	Liver
45	chr15:52444000-52451400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:52444000-52453600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:52444000-52455200	Weak transcription	Brain Anterior Caudate	brain
48	chr15:52444000-52455800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:52444000-52457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:52444000-52457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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