Variant report

Variant	rs4776008
Chromosome Location	chr15:52457227-52457228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11070882	0.81[ASN][1000 genomes]
rs11856177	0.81[ASN][1000 genomes]
rs12438169	0.92[ASN][1000 genomes]
rs12438190	0.83[ASN][1000 genomes]
rs12438274	0.84[ASN][1000 genomes]
rs12438937	0.92[ASN][1000 genomes]
rs12440354	0.92[ASN][1000 genomes]
rs12441074	0.92[ASN][1000 genomes]
rs12593041	0.92[ASN][1000 genomes]
rs12594679	0.94[EUR][1000 genomes]
rs12594809	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12898389	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12899030	0.89[ASN][1000 genomes]
rs12899343	0.89[ASN][1000 genomes]
rs12902522	0.92[ASN][1000 genomes]
rs12904880	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905698	0.90[ASN][1000 genomes]
rs12909184	0.92[ASN][1000 genomes]
rs12910052	0.90[ASN][1000 genomes]
rs12910398	0.92[ASN][1000 genomes]
rs12910870	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916557	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414130	0.82[ASN][1000 genomes]
rs2414132	0.89[ASN][1000 genomes]
rs34283892	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35709612	0.92[ASN][1000 genomes]
rs35733550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827106	0.81[ASN][1000 genomes]
rs35914910	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4238384	0.92[ASN][1000 genomes]
rs4506834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638520	0.90[ASN][1000 genomes]
rs4776007	0.92[ASN][1000 genomes]
rs4776012	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62014721	0.91[ASN][1000 genomes]
rs62014722	0.92[ASN][1000 genomes]
rs7166799	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181580	0.81[AMR][1000 genomes]
rs8026828	0.80[EUR][1000 genomes]
rs8029782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4776008	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs4776008	BCL2L10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

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	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:52439200-52463600	Weak transcription	NHEK	skin
7	chr15:52441000-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
12	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:52442400-52457800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:52442600-52470400	Weak transcription	HMEC	breast
16	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:52444000-52457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:52444000-52457800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:52444000-52458000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:52445600-52463400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:52445600-52463600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:52447400-52460200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
26	chr15:52447600-52463000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:52448000-52459800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:52448200-52457600	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:52448800-52465200	Weak transcription	Liver	Liver
30	chr15:52449200-52458200	Weak transcription	HepG2	liver
31	chr15:52452000-52463600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52454200-52464000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:52454400-52459200	Weak transcription	NHLF	lung
35	chr15:52454400-52463400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:52454400-52463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:52455800-52457400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:52455800-52458400	Weak transcription	Right Ventricle	heart
40	chr15:52455800-52463000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:52455800-52463400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:52455800-52463600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:52455800-52463600	Weak transcription	Primary B cells from cord blood	blood
44	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
45	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
46	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
47	chr15:52455800-52471000	Weak transcription	Gastric	stomach
48	chr15:52456000-52463000	Weak transcription	Fetal Thymus	thymus
49	chr15:52456000-52463400	Weak transcription	A549	lung
50	chr15:52456000-52464800	Weak transcription	Pancreas	Pancrea

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