Variant report

Variant	rs2864082
Chromosome Location	chr15:77527566-77527567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10519164	0.85[ASN][1000 genomes]
rs10519167	0.82[ASN][1000 genomes]
rs11630837	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630843	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631909	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632999	0.91[ASN][1000 genomes]
rs11633318	0.82[EUR][1000 genomes]
rs11634056	1.00[ASN][1000 genomes]
rs11636803	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637488	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638220	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639079	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639197	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639308	0.85[ASN][1000 genomes]
rs12899552	0.83[ASN][1000 genomes]
rs12909704	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910419	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554051	0.85[ASN][1000 genomes]
rs17382798	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17383727	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383984	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384406	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385648	0.85[ASN][1000 genomes]
rs17466989	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17468792	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17469276	0.83[ASN][1000 genomes]
rs17470228	0.85[ASN][1000 genomes]
rs2100054	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34672572	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34870981	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981488	0.82[ASN][1000 genomes]
rs35490414	0.85[ASN][1000 genomes]
rs35598964	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35902242	0.82[ASN][1000 genomes]
rs4450362	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55716459	0.82[ASN][1000 genomes]
rs56060493	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62007263	0.85[ASN][1000 genomes]
rs62008430	0.94[ASN][1000 genomes]
rs62008432	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008434	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62008455	0.82[EUR][1000 genomes]
rs6495233	0.80[AMR][1000 genomes]
rs66715204	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71405237	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71407208	0.85[ASN][1000 genomes]
rs7166293	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7176254	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181345	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182880	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030500	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8032925	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2864082	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
2	chr15:77480400-77528000	Weak transcription	Fetal Stomach	stomach
3	chr15:77482200-77528000	Weak transcription	Spleen	Spleen
4	chr15:77492200-77527800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:77492200-77527800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:77492200-77528200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
9	chr15:77507600-77528200	Weak transcription	Left Ventricle	heart
10	chr15:77508000-77543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:77509800-77528000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:77511200-77541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:77516800-77528200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:77517200-77528000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:77517200-77531600	Weak transcription	NHDF-Ad	bronchial
16	chr15:77517400-77528000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:77517400-77528000	Weak transcription	Aorta	Aorta
18	chr15:77517400-77559000	Weak transcription	Ovary	ovary
19	chr15:77517600-77527800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:77517600-77527800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:77517600-77528000	Weak transcription	Adipose Nuclei	Adipose
22	chr15:77517600-77528200	Weak transcription	HSMMtube	muscle
23	chr15:77517600-77528600	Weak transcription	Primary B cells from cord blood	blood
24	chr15:77517600-77543200	Weak transcription	HSMM	muscle
25	chr15:77517600-77545800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:77517800-77527600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:77517800-77527800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:77517800-77527800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:77517800-77528000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr15:77517800-77535400	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:77517800-77544200	Weak transcription	NHLF	lung
32	chr15:77518000-77528000	Weak transcription	Dnd41	blood
33	chr15:77518800-77528200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:77519200-77527800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:77519200-77528200	Weak transcription	Primary T cells from cord blood	blood
36	chr15:77519200-77528200	Weak transcription	Fetal Lung	lung
37	chr15:77519400-77530800	Weak transcription	Fetal Heart	heart
38	chr15:77519400-77551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:77519600-77551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:77519800-77527800	Weak transcription	HepG2	liver
41	chr15:77519800-77528000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:77519800-77557200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:77520000-77540000	Weak transcription	HUVEC	blood vessel
44	chr15:77520200-77527800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
46	chr15:77520400-77528000	Weak transcription	Fetal Intestine Small	intestine
47	chr15:77521200-77529400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:77521600-77529000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:77523000-77528200	Weak transcription	Esophagus	oesophagus
50	chr15:77523200-77544000	Weak transcription	Pancreas	Pancrea

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