Variant report

Variant	rs4636859
Chromosome Location	chr15:52435696-52435697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52435436-52436773	U87	brain:	n/a	n/a
2	POLR2A	chr15:52435340-52436752	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52433182..52434903-chr15:52435277..52437876,2	MCF-7	breast:

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070882	0.90[ASN][1000 genomes]
rs11856177	0.90[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12438190	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12438743	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12440956	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12594679	0.88[ASN][1000 genomes]
rs12595160	1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12899343	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12901354	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12901730	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12901891	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12902073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap]
rs12903769	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904831	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905698	0.80[EUR][1000 genomes]
rs12907835	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908742	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908833	0.90[ASN][1000 genomes]
rs12909161	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909184	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs12909880	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12910398	1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs12912428	0.92[ASN][1000 genomes]
rs12916557	0.90[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2398	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34283892	0.88[ASN][1000 genomes]
rs35709612	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35827106	0.90[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794543	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4774608	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776003	0.90[ASN][1000 genomes]
rs4776007	0.91[CEU][hapmap]
rs62014721	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62014722	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7164508	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs8034097	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs4636859	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:52417000-52436000	Weak transcription	Lung	lung
8	chr15:52417200-52436200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:52423000-52458200	Weak transcription	Dnd41	blood
12	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
14	chr15:52428800-52435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:52428800-52440600	Weak transcription	Spleen	Spleen
16	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
19	chr15:52429600-52438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:52429600-52440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:52429800-52436600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
23	chr15:52430000-52440800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:52430000-52441400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
26	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
27	chr15:52430200-52435800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:52430200-52437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:52430200-52438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:52430200-52440600	Weak transcription	Fetal Intestine Small	intestine
31	chr15:52430200-52441000	Weak transcription	Gastric	stomach
32	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
35	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
36	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
38	chr15:52430400-52436000	Weak transcription	NHEK	skin
39	chr15:52430400-52441200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
41	chr15:52431200-52437200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:52432200-52435800	Weak transcription	Fetal Thymus	thymus
44	chr15:52432200-52435800	Weak transcription	NHLF	lung
45	chr15:52432200-52436000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:52432200-52436000	Weak transcription	Placenta	Placenta
47	chr15:52432200-52436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:52432200-52438600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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