Variant report

Variant	rs12901730
Chromosome Location	chr15:52452697-52452698
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52430976..52433794-chr15:52452571..52454081,2	MCF-7	breast:
2	chr15:52450409..52453224-chr15:52453684..52455840,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000206995	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11070882	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11856177	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12438169	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs12438194	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12438743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12438937	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs12440354	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12440956	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12593041	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs12593939	0.82[AMR][1000 genomes]
rs12594679	0.88[ASN][1000 genomes]
rs12595160	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12899030	0.91[CEU][hapmap]
rs12899343	0.91[CEU][hapmap]
rs12901354	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12901891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902073	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]
rs12902522	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12903769	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12904831	0.83[AMR][1000 genomes]
rs12904889	0.89[ASN][1000 genomes]
rs12905698	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12907835	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12908742	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908833	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909161	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12909184	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909880	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12910052	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12910398	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912428	0.86[ASN][1000 genomes]
rs12916557	0.86[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap]
rs2398	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34283892	0.88[ASN][1000 genomes]
rs35827106	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3794540	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3794543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4238384	0.84[CHB][hapmap]
rs4636859	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4638520	0.91[CEU][hapmap]
rs4774608	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4776003	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4776007	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776010	0.81[AMR][1000 genomes]
rs4776011	0.89[AMR][1000 genomes]
rs4776014	0.81[AMR][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]
rs7166799	0.84[CHB][hapmap]
rs7172037	0.81[AMR][1000 genomes]
rs7177248	0.91[CHB][hapmap]
rs8034097	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[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
rs12901730	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr15:52443800-52453600	Weak transcription	Spleen	Spleen
36	chr15:52443800-52455200	Weak transcription	Right Ventricle	heart
37	chr15:52443800-52455400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:52443800-52456000	Weak transcription	Fetal Lung	lung
39	chr15:52443800-52457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:52444000-52453600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:52444000-52455200	Weak transcription	Brain Anterior Caudate	brain
43	chr15:52444000-52455800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:52444000-52457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:52444000-52457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:52444000-52457800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:52444000-52458000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:52444200-52455200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:52444400-52453800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr15:52445600-52453000	Weak transcription	Left Ventricle	heart

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