Variant report

Variant	rs690446
Chromosome Location	chr15:43761264-43761265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	15:43750262-43763629..15:43792489-43802874	K562	blood:
2	15:43750262-43763629..15:43802874-43806906	K562	blood:
3	chr15:43760402..43763686-chr15:43783244..43785576,3	K562	blood:
4	chr15:43756265..43758113-chr15:43760726..43762348,2	K562	blood:
5	chr15:43761184..43763590-chr15:43774247..43776021,2	K562	blood:
6	chr15:43760610..43763780-chr15:43765222..43770259,5	K562	blood:
7	15:43750262-43763629..15:44034348-44042259	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000067369	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000167004	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs101094	1.00[ASN][1000 genomes]
rs1058298	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060939	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1079309	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070399	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1133395	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11637572	0.85[AFR][1000 genomes]
rs11858640	1.00[ASN][1000 genomes]
rs12102205	0.80[EUR][1000 genomes]
rs12905772	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1814538	1.00[ASN][1000 genomes]
rs1869258	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012467	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2242069	0.98[ASN][1000 genomes]
rs2244746	0.84[EUR][1000 genomes]
rs2244981	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245054	1.00[ASN][1000 genomes]
rs2245176	1.00[ASN][1000 genomes]
rs2245664	0.98[ASN][1000 genomes]
rs2245780	1.00[ASN][1000 genomes]
rs2245785	0.92[ASN][1000 genomes]
rs2245790	1.00[ASN][1000 genomes]
rs2245908	0.98[ASN][1000 genomes]
rs2249952	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250743	0.98[ASN][1000 genomes]
rs2250750	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251538	1.00[ASN][1000 genomes]
rs2253268	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2253708	0.94[ASN][1000 genomes]
rs2253807	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2254321	0.95[ASN][1000 genomes]
rs2254325	0.94[ASN][1000 genomes]
rs2254927	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2255383	1.00[ASN][1000 genomes]
rs2255410	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2255663	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2264049	0.99[ASN][1000 genomes]
rs2264050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264239	1.00[ASN][1000 genomes]
rs2264248	0.97[ASN][1000 genomes]
rs2264876	1.00[ASN][1000 genomes]
rs2278856	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2278857	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2412781	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2439831	1.00[ASN][1000 genomes]
rs2439832	1.00[ASN][1000 genomes]
rs2439833	0.89[ASN][1000 genomes]
rs2439836	0.99[ASN][1000 genomes]
rs2439839	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439841	0.96[ASN][1000 genomes]
rs2439843	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439845	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439846	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439848	1.00[ASN][1000 genomes]
rs2439850	0.99[ASN][1000 genomes]
rs2444028	0.99[ASN][1000 genomes]
rs2444029	0.99[ASN][1000 genomes]
rs2444032	1.00[ASN][1000 genomes]
rs2444037	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2444247	0.99[ASN][1000 genomes]
rs2444249	0.97[ASN][1000 genomes]
rs2444250	1.00[ASN][1000 genomes]
rs2444251	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467736	1.00[ASN][1000 genomes]
rs2467737	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467738	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467739	1.00[ASN][1000 genomes]
rs2467740	1.00[ASN][1000 genomes]
rs2467741	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467742	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467743	1.00[ASN][1000 genomes]
rs2467745	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584694	0.94[ASN][1000 genomes]
rs2584700	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2584701	0.83[EUR][1000 genomes]
rs2584706	1.00[ASN][1000 genomes]
rs2584725	0.94[ASN][1000 genomes]
rs2584726	0.98[ASN][1000 genomes]
rs2584727	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2602141	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28649346	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28666488	1.00[ASN][1000 genomes]
rs2924368	0.98[ASN][1000 genomes]
rs2924369	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809482	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4296223	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4401024	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4547312	0.80[EUR][1000 genomes]
rs471229	0.99[ASN][1000 genomes]
rs478028	0.80[AMR][1000 genomes]
rs480108	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs483724	1.00[ASN][1000 genomes]
rs493377	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495175	0.94[ASN][1000 genomes]
rs506120	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509306	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518288	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523156	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs524417	1.00[ASN][1000 genomes]
rs526083	0.93[ASN][1000 genomes]
rs529611	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536313	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537115	0.99[ASN][1000 genomes]
rs542898	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548704	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550239	0.98[ASN][1000 genomes]
rs558656	0.98[ASN][1000 genomes]
rs560191	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561863	1.00[ASN][1000 genomes]
rs565007	0.97[ASN][1000 genomes]
rs570933	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs572837	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs573615	0.80[AMR][1000 genomes]
rs6493083	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493084	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493086	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689596	0.99[ASN][1000 genomes]
rs689616	1.00[ASN][1000 genomes]
rs689647	0.99[ASN][1000 genomes]
rs689693	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs689754	0.83[ASN][1000 genomes]
rs689767	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689781	0.94[ASN][1000 genomes]
rs689797	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689816	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs689826	1.00[ASN][1000 genomes]
rs689835	0.98[ASN][1000 genomes]
rs690002	0.91[ASN][1000 genomes]
rs690012	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs690038	0.94[ASN][1000 genomes]
rs690263	0.94[ASN][1000 genomes]
rs690276	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs690316	0.99[ASN][1000 genomes]
rs690367	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690436	1.00[ASN][1000 genomes]
rs690466	0.96[ASN][1000 genomes]
rs690472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690512	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693510	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694725	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166812	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7167882	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7170152	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7172374	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7497780	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8039671	0.83[ASN][1000 genomes]
rs8042688	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9920879	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs690446	AC011330.5	cis	Thyroid	GTEx
rs690446	ZSCAN29	cis	Thyroid	GTEx
rs690446	AC011330.5	cis	Artery Tibial	GTEx
rs690446	TGM5	cis	multi-tissue	Pritchard
rs690446	CKMT1A	cis	Esophagus Mucosa	GTEx
rs690446	ADAL	cis	Nerve Tibial	GTEx
rs690446	STRCP1	cis	Esophagus Muscularis	GTEx
rs690446	TGM7	cis	Esophagus Mucosa	GTEx
rs690446	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43726400-43769600	Weak transcription	Fetal Heart	heart
2	chr15:43730600-43765600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:43730600-43766800	Weak transcription	Small Intestine	intestine
4	chr15:43731200-43761400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:43734200-43780000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:43734200-43780200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:43739600-43761600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:43741600-43774800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:43743600-43763400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:43743800-43766800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:43743800-43770400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:43743800-43773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:43744000-43762600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:43744000-43770600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:43744000-43770600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:43744000-43773400	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:43744000-43773600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:43744000-43783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:43744000-43784000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:43746400-43782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:43746600-43773000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:43748000-43763400	Strong transcription	Dnd41	blood
23	chr15:43748800-43764800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:43749000-43766800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:43749200-43765000	Weak transcription	Esophagus	oesophagus
26	chr15:43749200-43765000	Weak transcription	Gastric	stomach
27	chr15:43749200-43767200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:43749200-43769800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:43749200-43784600	Weak transcription	Stomach Mucosa	stomach
30	chr15:43749400-43762600	Weak transcription	Brain Substantia Nigra	brain
31	chr15:43749400-43762800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:43749400-43764200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:43749400-43766600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:43749400-43766600	Weak transcription	HepG2	liver
35	chr15:43749400-43783800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:43749400-43784400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:43750400-43762400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:43750800-43765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:43751000-43765600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:43751000-43766000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:43751400-43775600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:43752400-43772400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:43752600-43765600	Weak transcription	Pancreas	Pancrea
44	chr15:43752600-43767400	Weak transcription	Fetal Brain Male	brain
45	chr15:43752800-43765000	Weak transcription	Aorta	Aorta
46	chr15:43752800-43766000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:43752800-43775200	Strong transcription	Placenta	Placenta
48	chr15:43753600-43761400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:43754400-43770600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:43754600-43763200	Strong transcription	Fetal Thymus	thymus

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