Variant report

Variant	rs4401024
Chromosome Location	chr15:43650335-43650336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43476605..43479109-chr15:43648821..43650623,2	K562	blood:

Variant related genes	Relation type
ENSG00000166946	Chromatin interaction
ENSG00000261687	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1058298	0.83[EUR][1000 genomes]
rs1079309	0.80[AMR][1000 genomes]
rs1095386	0.95[ASN][1000 genomes]
rs11070399	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123947	0.99[ASN][1000 genomes]
rs1133395	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637572	0.82[EUR][1000 genomes]
rs11858152	0.96[ASN][1000 genomes]
rs12101673	0.97[ASN][1000 genomes]
rs12102205	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148735	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12323999	0.91[ASN][1000 genomes]
rs12324572	0.99[ASN][1000 genomes]
rs12324584	0.91[ASN][1000 genomes]
rs12905772	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549523	0.99[ASN][1000 genomes]
rs1549525	0.99[ASN][1000 genomes]
rs16957627	0.99[ASN][1000 genomes]
rs16957630	0.99[ASN][1000 genomes]
rs16957632	0.99[ASN][1000 genomes]
rs1837959	0.85[ASN][1000 genomes]
rs1837960	0.85[ASN][1000 genomes]
rs2012467	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242068	0.83[ASN][1000 genomes]
rs2243434	0.87[ASN][1000 genomes]
rs2244746	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2244981	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2249952	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2253268	0.80[AMR][1000 genomes]
rs2253807	0.85[AMR][1000 genomes]
rs2264050	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2278856	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278857	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278859	0.99[ASN][1000 genomes]
rs2278860	0.99[ASN][1000 genomes]
rs2412778	0.99[ASN][1000 genomes]
rs2412779	0.99[ASN][1000 genomes]
rs2412780	0.99[ASN][1000 genomes]
rs2412781	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412782	0.88[ASN][1000 genomes]
rs2439845	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2439846	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2444036	0.88[ASN][1000 genomes]
rs2444037	0.84[EUR][1000 genomes]
rs2444251	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2467733	0.88[ASN][1000 genomes]
rs2467737	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2467738	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467741	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2467742	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467745	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2584700	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2584701	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2584702	0.91[ASN][1000 genomes]
rs2584703	0.85[ASN][1000 genomes]
rs2584727	0.80[AMR][1000 genomes]
rs2602141	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28415933	0.99[ASN][1000 genomes]
rs28461955	0.99[ASN][1000 genomes]
rs28649346	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28653441	0.94[ASN][1000 genomes]
rs28702649	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28729853	0.94[ASN][1000 genomes]
rs2899082	0.99[ASN][1000 genomes]
rs2924369	0.80[AMR][1000 genomes]
rs3213990	0.94[ASN][1000 genomes]
rs3213991	0.95[ASN][1000 genomes]
rs3742969	0.97[ASN][1000 genomes]
rs3742971	0.97[ASN][1000 genomes]
rs3809482	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4075674	0.99[ASN][1000 genomes]
rs4296223	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547312	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4583210	0.99[ASN][1000 genomes]
rs478028	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478104	0.89[ASN][1000 genomes]
rs484029	0.97[ASN][1000 genomes]
rs484846	0.90[ASN][1000 genomes]
rs485148	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs488756	0.95[ASN][1000 genomes]
rs491800	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs493377	0.80[AMR][1000 genomes]
rs498837	0.91[ASN][1000 genomes]
rs499035	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs507178	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509306	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510108	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs511673	0.97[ASN][1000 genomes]
rs512628	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518288	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs528517	0.95[ASN][1000 genomes]
rs536313	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs538238	0.87[EUR][1000 genomes]
rs540031	0.95[ASN][1000 genomes]
rs542898	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs548704	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs552701	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs560191	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs573615	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs576557	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493081	0.98[ASN][1000 genomes]
rs6493082	0.99[ASN][1000 genomes]
rs6493083	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493085	0.99[ASN][1000 genomes]
rs6493086	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493087	0.83[ASN][1000 genomes]
rs6493088	0.95[ASN][1000 genomes]
rs689693	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689767	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690012	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs690276	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690367	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690446	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690472	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690512	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs693510	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694725	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7163245	0.94[ASN][1000 genomes]
rs7165471	0.99[ASN][1000 genomes]
rs7166812	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167882	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168940	0.96[ASN][1000 genomes]
rs7170152	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170489	0.99[ASN][1000 genomes]
rs7172374	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175434	0.97[ASN][1000 genomes]
rs7176849	0.91[ASN][1000 genomes]
rs8033714	0.97[ASN][1000 genomes]
rs8039638	0.96[ASN][1000 genomes]
rs8041132	0.99[ASN][1000 genomes]
rs8042688	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825739	0.86[ASN][1000 genomes]
rs825740	0.86[ASN][1000 genomes]
rs884704	0.89[ASN][1000 genomes]
rs933941	0.99[ASN][1000 genomes]
rs956391	0.97[ASN][1000 genomes]
rs9920879	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs999026	0.88[ASN][1000 genomes]
rs999047	0.88[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
rs4401024	ZSCAN29	cis	Thyroid	GTEx
rs4401024	TGM7	cis	Esophagus Mucosa	GTEx
rs4401024	AC011330.5	cis	Thyroid	GTEx
rs4401024	ADAL	cis	Nerve Tibial	GTEx
rs4401024	TGM5	cis	multi-tissue	Pritchard
rs4401024	STRCP1	cis	Esophagus Muscularis	GTEx
rs4401024	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 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	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
5	chr15:43623400-43651000	Weak transcription	Gastric	stomach
6	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
7	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:43623600-43650400	Weak transcription	NH-A	brain
9	chr15:43623600-43650800	Weak transcription	HMEC	breast
10	chr15:43623600-43650800	Weak transcription	NHLF	lung
11	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:43623600-43651000	Weak transcription	A549	lung
13	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:43628400-43650400	Weak transcription	Primary B cells from cord blood	blood
15	chr15:43629200-43651000	Weak transcription	NHDF-Ad	bronchial
16	chr15:43630400-43650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:43630800-43650600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:43631600-43650400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:43631800-43651000	Weak transcription	Esophagus	oesophagus
20	chr15:43633200-43650600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:43633800-43650800	Weak transcription	Osteobl	bone
22	chr15:43634000-43651000	Weak transcription	Aorta	Aorta
23	chr15:43635400-43651000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:43639800-43650400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:43640400-43651000	Weak transcription	Fetal Kidney	kidney
26	chr15:43641200-43652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:43641400-43650600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:43641600-43652800	Weak transcription	Hela-S3	cervix
29	chr15:43642200-43650800	Weak transcription	NHEK	skin
30	chr15:43643000-43651800	Weak transcription	Colonic Mucosa	Colon
31	chr15:43643400-43652800	Weak transcription	Right Ventricle	heart
32	chr15:43643600-43650400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:43643600-43650400	Weak transcription	Fetal Lung	lung
34	chr15:43643800-43650800	Weak transcription	Ovary	ovary
35	chr15:43644400-43650400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:43644400-43650800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:43644400-43650800	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:43644400-43650800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:43644400-43650800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:43644400-43650800	Weak transcription	HepG2	liver
41	chr15:43644400-43651000	Weak transcription	Brain Angular Gyrus	brain
42	chr15:43644400-43651000	Weak transcription	Spleen	Spleen
43	chr15:43644400-43651800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:43644600-43650400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:43644600-43650800	Weak transcription	Brain Substantia Nigra	brain
46	chr15:43644800-43650800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:43644800-43651000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:43644800-43651000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:43644800-43651000	Weak transcription	Thymus	Thymus
50	chr15:43645000-43650400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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