Variant report

Variant	rs7546661
Chromosome Location	chr1:93840757-93840758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1000606	0.89[EUR][1000 genomes]
rs10430073	0.89[EUR][1000 genomes]
rs10782958	0.89[EUR][1000 genomes]
rs1081523	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081524	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081526	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10874765	0.89[EUR][1000 genomes]
rs10874767	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874771	0.89[EUR][1000 genomes]
rs10874774	0.84[EUR][1000 genomes]
rs10874775	0.95[EUR][1000 genomes]
rs1088319	0.81[EUR][1000 genomes]
rs11164888	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164889	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164890	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164891	0.86[EUR][1000 genomes]
rs11164906	0.89[EUR][1000 genomes]
rs11164911	0.94[EUR][1000 genomes]
rs11582703	0.89[EUR][1000 genomes]
rs11584466	0.89[EUR][1000 genomes]
rs12070900	0.89[EUR][1000 genomes]
rs12071627	0.89[EUR][1000 genomes]
rs12080715	0.89[EUR][1000 genomes]
rs12085959	0.89[EUR][1000 genomes]
rs12090723	0.89[EUR][1000 genomes]
rs12731675	0.89[EUR][1000 genomes]
rs12731809	0.89[EUR][1000 genomes]
rs1323626	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1323627	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1323628	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1535698	0.89[EUR][1000 genomes]
rs1535700	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1570528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2031223	0.95[EUR][1000 genomes]
rs2031224	0.89[EUR][1000 genomes]
rs2104280	0.88[EUR][1000 genomes]
rs2815414	0.83[AMR][1000 genomes]
rs3767965	0.87[ASN][1000 genomes]
rs4573531	0.89[EUR][1000 genomes]
rs4847239	0.93[EUR][1000 genomes]
rs4847407	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847409	0.89[EUR][1000 genomes]
rs4847411	0.95[EUR][1000 genomes]
rs485622	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs488646	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs504810	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs506556	0.83[AMR][1000 genomes]
rs508942	0.87[EUR][1000 genomes]
rs512361	0.89[EUR][1000 genomes]
rs519723	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs523262	0.87[EUR][1000 genomes]
rs556888	0.89[EUR][1000 genomes]
rs558667	0.88[EUR][1000 genomes]
rs559397	0.89[EUR][1000 genomes]
rs56303209	0.89[EUR][1000 genomes]
rs566743	0.84[EUR][1000 genomes]
rs571212	0.81[EUR][1000 genomes]
rs587754	0.89[EUR][1000 genomes]
rs605759	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs626714	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs628714	0.86[EUR][1000 genomes]
rs629153	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs631966	0.89[EUR][1000 genomes]
rs633789	0.89[EUR][1000 genomes]
rs637198	0.87[EUR][1000 genomes]
rs641390	0.87[EUR][1000 genomes]
rs6541351	0.95[EUR][1000 genomes]
rs6541400	0.89[EUR][1000 genomes]
rs658178	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs661566	0.83[EUR][1000 genomes]
rs662546	0.83[EUR][1000 genomes]
rs6657587	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6664886	0.94[EUR][1000 genomes]
rs6667701	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs667680	0.82[AMR][1000 genomes]
rs6687359	0.89[EUR][1000 genomes]
rs668944	0.86[EUR][1000 genomes]
rs6701250	0.83[EUR][1000 genomes]
rs670650	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs693872	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs698926	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7413775	0.89[EUR][1000 genomes]
rs7519163	0.89[EUR][1000 genomes]
rs7525189	0.89[EUR][1000 genomes]
rs7529639	0.97[EUR][1000 genomes]
rs7551635	0.89[EUR][1000 genomes]
rs7555292	0.89[EUR][1000 genomes]
rs771448	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771449	0.97[EUR][1000 genomes]
rs771450	0.97[EUR][1000 genomes]
rs771451	0.97[EUR][1000 genomes]
rs771452	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771453	0.97[EUR][1000 genomes]
rs771455	0.82[EUR][1000 genomes]
rs771456	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs771457	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771459	0.94[EUR][1000 genomes]
rs771460	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771463	0.94[EUR][1000 genomes]
rs771464	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771466	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771471	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771472	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771474	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771480	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs797669	0.82[EUR][1000 genomes]
rs809515	0.81[EUR][1000 genomes]
rs810028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9432680	0.88[EUR][1000 genomes]
rs9432700	0.89[EUR][1000 genomes]
rs9432701	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7546661	RP4-717I23.3	cis	Thyroid	GTEx
rs7546661	RP4-717I23.3	cis	Artery Tibial	GTEx
rs7546661	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs7546661	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs7546661	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs7546661	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs7546661	RP4-717I23.3	cis	Whole Blood	GTEx
rs7546661	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs7546661	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs7546661	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7546661	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs7546661	RP4-717I23.3	cis	lung	GTEx
rs7546661	RP4-717I23.3	cis	Artery Aorta	GTEx
rs7546661	RP4-717I23.3	cis	Stomach	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93816600-93841800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:93816800-93841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:93824200-93841000	Weak transcription	Brain Germinal Matrix	brain
4	chr1:93824200-93841000	Weak transcription	Spleen	Spleen
5	chr1:93824400-93842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:93825200-93840800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:93826200-93841400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:93828200-93842400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:93829200-93843600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:93831600-93841000	Weak transcription	NHEK	skin
11	chr1:93833200-93841200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:93833200-93841200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:93833200-93841400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:93833400-93841000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:93833400-93841200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:93833400-93841200	Weak transcription	Fetal Intestine Large	intestine
17	chr1:93833600-93840800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:93833800-93841400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:93834200-93841200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:93834200-93841400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:93834200-93841400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:93834200-93848200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:93834400-93841400	Weak transcription	Fetal Lung	lung
24	chr1:93834400-93842400	Weak transcription	Primary B cells from cord blood	blood
25	chr1:93835800-93850400	Weak transcription	Dnd41	blood
26	chr1:93836000-93841000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:93836000-93843400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:93836000-93848000	Weak transcription	HSMM	muscle
29	chr1:93836800-93840800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:93837800-93841000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:93838800-93840800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:93839400-93840800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
33	chr1:93839400-93841000	Strong transcription	Fetal Intestine Small	intestine
34	chr1:93839400-93841600	Strong transcription	Thymus	Thymus
35	chr1:93839600-93840800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:93839600-93841200	Strong transcription	Primary T cells from cord blood	blood
37	chr1:93839800-93840800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:93839800-93841400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:93840000-93840800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
40	chr1:93840000-93840800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:93840000-93841200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:93840200-93841400	Weak transcription	Adipose Nuclei	Adipose
43	chr1:93840200-93851400	Weak transcription	Left Ventricle	heart
44	chr1:93840400-93840800	Weak transcription	Fetal Stomach	stomach
45	chr1:93840400-93841000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:93840400-93841200	ZNF genes & repeats	Placenta	Placenta
47	chr1:93840600-93840800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
48	chr1:93840600-93841000	Enhancers	Right Ventricle	heart
49	chr1:93840600-93841000	Strong transcription	A549	lung
50	chr1:93840600-93843400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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