Variant report

Variant	rs7164508
Chromosome Location	chr15:52477809-52477810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52469294..52473868-chr15:52474037..52480936,12	MCF-7	breast:
2	chr15:52477307..52479865-chr15:52479877..52482312,2	MCF-7	breast:
3	chr15:52475782..52478747-chr15:52482859..52485201,2	MCF-7	breast:
4	chr15:52477453..52480086-chr15:52495513..52498158,2	K562	blood:
5	chr15:52477215..52477900-chr15:52500295..52500830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1077383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070882	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11855672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856177	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438194	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12438743	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12593936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593939	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595160	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901730	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12901891	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12902073	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12902522	1.00[CEU][hapmap]
rs12903539	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12903769	0.86[AMR][1000 genomes]
rs12907835	1.00[YRI][hapmap]
rs12908742	0.80[AMR][1000 genomes]
rs12909161	1.00[YRI][hapmap]
rs12909184	1.00[YRI][hapmap]
rs12909880	0.80[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12916135	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap]
rs2398	1.00[YRI][hapmap]
rs34276836	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35712143	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35827106	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794540	1.00[YRI][hapmap]
rs4636859	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4774612	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4776010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776011	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776013	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776014	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66566761	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67163040	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67447954	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67725996	0.90[EUR][1000 genomes]
rs71472930	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7172037	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183278	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025701	0.86[CHB][hapmap]
rs8025737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8034097	1.00[YRI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7164508	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473000-52478400	Weak transcription	Aorta	Aorta
2	chr15:52473000-52479200	Weak transcription	Right Atrium	heart
3	chr15:52473000-52479400	Weak transcription	Esophagus	oesophagus
4	chr15:52473000-52483800	Weak transcription	A549	lung
5	chr15:52473000-52489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52473200-52478600	Weak transcription	Lung	lung
7	chr15:52473200-52479400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:52473200-52483600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52473200-52483600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:52473200-52483800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:52473400-52478600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:52473400-52483400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:52473400-52483600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:52473400-52485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:52473400-52496400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:52473400-52496400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:52473400-52496600	Weak transcription	Spleen	Spleen
19	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:52474600-52488400	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:52475400-52483600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:52475800-52478000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:52475800-52479400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:52476600-52478000	Enhancers	Liver	Liver
26	chr15:52476800-52484200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:52477200-52478000	Enhancers	Pancreas	Pancrea
28	chr15:52477200-52479800	Enhancers	Ovary	ovary
29	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
31	chr15:52477800-52478800	Weak transcription	HepG2	liver
32	chr15:52477800-52483400	Weak transcription	Fetal Intestine Small	intestine
33	chr15:52477800-52488000	Weak transcription	Gastric	stomach
34	chr15:52477800-52494800	Weak transcription	Fetal Intestine Large	intestine

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