Variant report

Variant	rs11070399
Chromosome Location	chr15:43646347-43646348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43646115..43650025-chr15:43654953..43659195,5	K562	blood:
2	chr15:43645456..43647561-chr15:43650775..43652983,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1058298	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1095386	0.97[ASN][1000 genomes]
rs1123947	1.00[ASN][1000 genomes]
rs1133395	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637572	0.82[EUR][1000 genomes]
rs11858152	0.97[ASN][1000 genomes]
rs12101673	0.98[ASN][1000 genomes]
rs12102205	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148735	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12323999	0.92[ASN][1000 genomes]
rs12324572	1.00[ASN][1000 genomes]
rs12324584	0.92[ASN][1000 genomes]
rs12905772	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549523	1.00[ASN][1000 genomes]
rs1549525	1.00[ASN][1000 genomes]
rs16957627	1.00[ASN][1000 genomes]
rs16957630	1.00[ASN][1000 genomes]
rs16957632	1.00[ASN][1000 genomes]
rs1837959	0.87[ASN][1000 genomes]
rs1837960	0.87[ASN][1000 genomes]
rs2012467	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242068	0.84[ASN][1000 genomes]
rs2243434	0.88[ASN][1000 genomes]
rs2244746	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2244981	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2249952	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2253807	0.84[AMR][1000 genomes]
rs2264050	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2278856	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278857	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278859	1.00[ASN][1000 genomes]
rs2278860	1.00[ASN][1000 genomes]
rs2412778	1.00[ASN][1000 genomes]
rs2412779	1.00[ASN][1000 genomes]
rs2412780	1.00[ASN][1000 genomes]
rs2412781	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412782	0.90[ASN][1000 genomes]
rs2439845	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2439846	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2444036	0.89[ASN][1000 genomes]
rs2444037	0.84[EUR][1000 genomes]
rs2444251	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2467733	0.89[ASN][1000 genomes]
rs2467737	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2467738	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467741	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2467742	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467745	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2584700	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2584701	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2584702	0.92[ASN][1000 genomes]
rs2584703	0.87[ASN][1000 genomes]
rs2602141	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28415933	1.00[ASN][1000 genomes]
rs28461955	1.00[ASN][1000 genomes]
rs28649346	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28653441	0.95[ASN][1000 genomes]
rs28702649	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729853	0.95[ASN][1000 genomes]
rs2899082	1.00[ASN][1000 genomes]
rs3213990	0.96[ASN][1000 genomes]
rs3213991	0.97[ASN][1000 genomes]
rs3742969	0.99[ASN][1000 genomes]
rs3742971	0.99[ASN][1000 genomes]
rs3809482	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075674	1.00[ASN][1000 genomes]
rs4296223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4401024	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547312	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583210	1.00[ASN][1000 genomes]
rs478028	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478104	0.90[ASN][1000 genomes]
rs484029	0.99[ASN][1000 genomes]
rs484846	0.92[ASN][1000 genomes]
rs485148	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs488756	0.97[ASN][1000 genomes]
rs491800	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs498837	0.92[ASN][1000 genomes]
rs499035	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs507178	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509306	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510108	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511673	0.99[ASN][1000 genomes]
rs512628	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513970	0.81[AMR][1000 genomes]
rs518288	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs528517	0.97[ASN][1000 genomes]
rs536313	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs538238	0.87[EUR][1000 genomes]
rs540031	0.97[ASN][1000 genomes]
rs542898	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs548704	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs552701	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560191	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs573615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576557	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493081	0.99[ASN][1000 genomes]
rs6493082	1.00[ASN][1000 genomes]
rs6493083	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493085	1.00[ASN][1000 genomes]
rs6493086	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493087	0.82[ASN][1000 genomes]
rs6493088	0.97[ASN][1000 genomes]
rs689693	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689767	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690012	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690276	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690367	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690446	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690472	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690512	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs693510	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694725	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7163245	0.95[ASN][1000 genomes]
rs7165471	1.00[ASN][1000 genomes]
rs7166812	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167882	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168940	0.97[ASN][1000 genomes]
rs7170152	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170489	1.00[ASN][1000 genomes]
rs7172374	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175434	0.99[ASN][1000 genomes]
rs7176849	0.92[ASN][1000 genomes]
rs8033714	0.96[ASN][1000 genomes]
rs8039638	0.97[ASN][1000 genomes]
rs8041132	1.00[ASN][1000 genomes]
rs8042688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825739	0.87[ASN][1000 genomes]
rs825740	0.87[ASN][1000 genomes]
rs884704	0.90[ASN][1000 genomes]
rs933941	1.00[ASN][1000 genomes]
rs956391	0.98[ASN][1000 genomes]
rs9920879	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999026	0.90[ASN][1000 genomes]
rs999047	0.90[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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11070399	ADAL	cis	Nerve Tibial	GTEx
rs11070399	ZSCAN29	cis	Thyroid	GTEx
rs11070399	TGM7	cis	Esophagus Mucosa	GTEx
rs11070399	STRCP1	cis	Esophagus Muscularis	GTEx
rs11070399	AC011330.5	cis	Thyroid	GTEx
rs11070399	ZSCAN29	cis	multi-tissue	Pritchard
rs11070399	TGM5	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43651000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
4	chr15:43623400-43649200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
6	chr15:43623400-43651000	Weak transcription	Gastric	stomach
7	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
8	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:43623600-43646600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:43623600-43646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:43623600-43650400	Weak transcription	NH-A	brain
12	chr15:43623600-43650800	Weak transcription	HMEC	breast
13	chr15:43623600-43650800	Weak transcription	NHLF	lung
14	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:43623600-43651000	Weak transcription	A549	lung
16	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:43624000-43647000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:43625600-43647200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:43628400-43650400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:43629200-43651000	Weak transcription	NHDF-Ad	bronchial
21	chr15:43630200-43650200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:43630400-43650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:43630800-43650600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:43631600-43650400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:43631800-43651000	Weak transcription	Esophagus	oesophagus
26	chr15:43633200-43650600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:43633800-43650800	Weak transcription	Osteobl	bone
28	chr15:43634000-43651000	Weak transcription	Aorta	Aorta
29	chr15:43635200-43646600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:43635400-43651000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:43637200-43647200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:43638000-43646400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:43639800-43650400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:43640400-43651000	Weak transcription	Fetal Kidney	kidney
35	chr15:43641000-43647200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:43641200-43646400	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:43641200-43652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:43641400-43650200	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:43641400-43650600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:43641600-43649800	Weak transcription	Placenta	Placenta
41	chr15:43641600-43652800	Weak transcription	Hela-S3	cervix
42	chr15:43641800-43646600	Strong transcription	Fetal Stomach	stomach
43	chr15:43642000-43646400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:43642200-43650800	Weak transcription	NHEK	skin
45	chr15:43642400-43647000	Weak transcription	Fetal Intestine Small	intestine
46	chr15:43642800-43648200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:43643000-43651800	Weak transcription	Colonic Mucosa	Colon
48	chr15:43643400-43652800	Weak transcription	Right Ventricle	heart
49	chr15:43643600-43650400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:43643600-43650400	Weak transcription	Fetal Lung	lung

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