Variant report

Variant	rs35712143
Chromosome Location	chr15:52469856-52469857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52465292..52467167-chr15:52468410..52470293,2	MCF-7	breast:
2	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
3	chr15:52262628..52265811-chr15:52469801..52473537,4	MCF-7	breast:
4	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
5	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
6	chr15:52469037..52470714-chr15:52511840..52513591,2	MCF-7	breast:
7	chr15:52464249..52467192-chr15:52469129..52471507,3	K562	blood:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1077383	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11070882	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11855672	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11856177	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12593936	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593939	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595160	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12903539	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12916135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964750	0.86[AFR][1000 genomes]
rs34276836	0.91[ASN][1000 genomes]
rs35827106	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4774612	0.84[ASN][1000 genomes]
rs4776010	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776011	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776014	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59289747	0.83[AFR][1000 genomes]
rs66566761	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67163040	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67447954	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67725996	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71472930	0.84[ASN][1000 genomes]
rs7164508	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165708	0.80[AFR][1000 genomes]
rs7172037	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73404813	0.82[AFR][1000 genomes]
rs8024311	0.83[AFR][1000 genomes]
rs8025737	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8040458	0.81[AFR][1000 genomes]
rs8041504	0.83[AFR][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
rs35712143	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52442600-52470400	Weak transcription	HMEC	breast
7	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
10	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
12	chr15:52455800-52471000	Weak transcription	Gastric	stomach
13	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
17	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
19	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
21	chr15:52463200-52470600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:52463600-52470400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:52463800-52470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:52464000-52470000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:52464000-52470200	Weak transcription	NHEK	skin
26	chr15:52464000-52470800	Weak transcription	HUVEC	blood vessel
27	chr15:52464000-52471000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:52464200-52470200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:52464200-52470400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:52464400-52470000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:52464400-52470000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:52464400-52470200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:52464400-52470400	Weak transcription	Primary T cells from cord blood	blood
34	chr15:52464400-52470600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:52464400-52470600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr15:52464800-52470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:52465600-52470600	Weak transcription	Liver	Liver
38	chr15:52465800-52470600	Weak transcription	Pancreas	Pancrea
39	chr15:52467200-52470000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:52467400-52470600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:52467600-52470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:52468400-52470800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr15:52468600-52470400	Weak transcription	GM12878-XiMat	blood
44	chr15:52468600-52470800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr15:52468800-52470000	Weak transcription	Hela-S3	cervix
46	chr15:52468800-52470200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:52468800-52470600	Weak transcription	Brain Angular Gyrus	brain
48	chr15:52469000-52470000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:52469000-52470000	Weak transcription	Thymus	Thymus
50	chr15:52469000-52470200	Weak transcription	Primary B cells from cord blood	blood

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