Variant report

Variant	rs12910419
Chromosome Location	chr15:77451350-77451351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11630837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630843	0.91[ASN][1000 genomes]
rs11631909	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11634056	0.91[ASN][1000 genomes]
rs11636803	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637488	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11638220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639079	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639197	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904384	1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs12909704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17382798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383727	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17383984	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17384406	0.91[ASN][1000 genomes]
rs17466989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468792	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2100054	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864082	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33940778	0.85[JPT][hapmap]
rs34672572	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34870981	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35598964	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4450362	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56060493	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62008430	0.85[ASN][1000 genomes]
rs62008432	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62008434	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6495233	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66715204	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71405237	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166293	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7176254	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181345	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182880	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030500	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032925	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12910419	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx
rs12910419	RP11-797A18.4	cis	Skin Sun Exposed Lower leg	GTEx
rs12910419	SGK269	cis	parietal	SCAN
rs12910419	HMG20A	cis	parietal	SCAN
rs12910419	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
2	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
4	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
5	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
6	chr15:77437000-77451600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:77437000-77451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:77437600-77453400	Weak transcription	HMEC	breast
10	chr15:77438000-77453200	Weak transcription	Fetal Heart	heart
11	chr15:77438000-77453400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:77438400-77461000	Weak transcription	NH-A	brain
13	chr15:77438600-77457600	Weak transcription	Gastric	stomach
14	chr15:77438600-77461400	Weak transcription	Aorta	Aorta
15	chr15:77438600-77469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:77438600-77470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:77439800-77460600	Weak transcription	HSMMtube	muscle
18	chr15:77440200-77453000	Weak transcription	Fetal Kidney	kidney
19	chr15:77444200-77460600	Weak transcription	NHEK	skin
20	chr15:77445200-77461000	Weak transcription	Small Intestine	intestine
21	chr15:77446400-77454600	Weak transcription	Esophagus	oesophagus
22	chr15:77447800-77453800	Weak transcription	K562	blood
23	chr15:77447800-77456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:77448000-77452400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:77448200-77452400	Weak transcription	Fetal Thymus	thymus
26	chr15:77448200-77457400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:77448400-77452000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:77448600-77451400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:77448600-77452400	Weak transcription	Lung	lung
30	chr15:77448800-77452000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:77448800-77452200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:77448800-77452200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:77448800-77453000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr15:77449000-77451800	Weak transcription	Fetal Intestine Small	intestine
35	chr15:77449000-77465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:77449200-77451400	Strong transcription	Primary B cells from cord blood	blood
37	chr15:77449200-77451400	Strong transcription	NHDF-Ad	bronchial
38	chr15:77449200-77451600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:77449200-77452000	Strong transcription	Osteobl	bone
40	chr15:77449400-77452600	Weak transcription	HepG2	liver
41	chr15:77449600-77453600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:77449800-77453200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:77450000-77451400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr15:77450000-77452400	Weak transcription	Fetal Stomach	stomach
45	chr15:77450000-77453200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:77450000-77453400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:77450000-77453400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:77450000-77455200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr15:77450000-77458000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:77450000-77460600	Weak transcription	Left Ventricle	heart

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