Variant report

Variant	rs602204
Chromosome Location	chr1:93727579-93727580
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	chr1:93725585..93728395-chr1:93728407..93730397,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1000607	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1057257	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782955	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10782957	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874759	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10874762	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10874772	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874773	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874777	0.86[EUR][1000 genomes]
rs1088318	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164876	0.85[EUR][1000 genomes]
rs11164879	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164880	0.87[EUR][1000 genomes]
rs11164881	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164885	0.80[ASN][1000 genomes]
rs11164902	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164904	0.91[ASN][1000 genomes]
rs11576494	0.85[EUR][1000 genomes]
rs12030549	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030843	0.80[ASN][1000 genomes]
rs12031765	0.80[ASN][1000 genomes]
rs12044557	0.80[ASN][1000 genomes]
rs12044657	0.88[EUR][1000 genomes]
rs12044883	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118230	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118262	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124011	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124771	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12130734	0.84[EUR][1000 genomes]
rs12133576	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12139633	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405487	0.80[ASN][1000 genomes]
rs12406245	0.87[EUR][1000 genomes]
rs12752223	0.81[ASN][1000 genomes]
rs1335679	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1426318	0.87[EUR][1000 genomes]
rs1535699	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1535701	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1559828	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572343	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1593512	0.87[EUR][1000 genomes]
rs1932314	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2031225	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031226	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2152358	0.83[AMR][1000 genomes]
rs2295423	0.80[AMR][1000 genomes]
rs2296558	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297707	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391251	0.80[ASN][1000 genomes]
rs2391254	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765545	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35940311	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3754186	0.94[ASN][1000 genomes]
rs3767962	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3767964	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904665	0.80[ASN][1000 genomes]
rs4000699	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240966	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4484937	0.80[ASN][1000 genomes]
rs4847235	0.85[EUR][1000 genomes]
rs4847240	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847402	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847406	0.94[ASN][1000 genomes]
rs4847408	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847410	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847412	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847419	0.87[EUR][1000 genomes]
rs4847420	0.87[EUR][1000 genomes]
rs531358	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs531514	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs535760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547866	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555161	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs565919	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569414	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58354545	0.80[ASN][1000 genomes]
rs59417472	0.87[EUR][1000 genomes]
rs612037	0.82[EUR][1000 genomes]
rs61799500	0.80[ASN][1000 genomes]
rs61799516	0.80[ASN][1000 genomes]
rs622608	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs624131	0.82[EUR][1000 genomes]
rs627779	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs637646	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541349	0.85[ASN][1000 genomes]
rs6541401	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6541404	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658257	0.82[ASN][1000 genomes]
rs6676902	0.80[ASN][1000 genomes]
rs6680022	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6680107	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682670	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6684908	0.80[ASN][1000 genomes]
rs6688230	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6694508	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6703310	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs682514	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687394	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs693737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959220	0.80[ASN][1000 genomes]
rs7417952	0.87[EUR][1000 genomes]
rs7418101	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7512911	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7513705	0.89[EUR][1000 genomes]
rs7517363	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7524964	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7525248	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7526112	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532195	0.85[EUR][1000 genomes]
rs7535628	0.87[EUR][1000 genomes]
rs7537403	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539307	0.88[EUR][1000 genomes]
rs7540025	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541304	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541687	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547244	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7551485	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553465	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553916	0.83[ASN][1000 genomes]
rs797661	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs797666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs797668	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs797671	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs797672	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797676	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797680	0.81[AMR][1000 genomes]
rs797681	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942196	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432453	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9432459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9432465	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9432681	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9660390	0.80[AMR][1000 genomes];0.88[ASN][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	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs602204	RP4-717I23.3	cis	Artery Tibial	GTEx
rs602204	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs602204	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs602204	RP4-717I23.3	cis	Thyroid	GTEx
rs602204	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs602204	RP4-717I23.3	cis	lung	GTEx
rs602204	RP4-717I23.3	cis	Whole Blood	GTEx
rs602204	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs602204	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs602204	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs602204	CCDC18	cis	Nerve Tibial	GTEx
rs602204	DR1	cis	Adipose Subcutaneous	GTEx
rs602204	DR1	cis	multi-tissue	Pritchard
rs602204	RP4-717I23.3	cis	Artery Aorta	GTEx
rs602204	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs602204	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs602204	RP4-717I23.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
5	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
7	chr1:93709000-93728200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:93709000-93728200	Weak transcription	HMEC	breast
9	chr1:93709400-93727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:93716200-93728400	Weak transcription	Pancreas	Pancrea
11	chr1:93716800-93727600	Weak transcription	Fetal Kidney	kidney
12	chr1:93717800-93727800	Weak transcription	Ovary	ovary
13	chr1:93718600-93727800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:93718600-93728200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:93718800-93728000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:93718800-93728200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:93718800-93728200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:93719000-93727600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:93719000-93727600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:93719000-93728000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:93719200-93727600	Weak transcription	Aorta	Aorta
22	chr1:93719200-93728200	Weak transcription	A549	lung
23	chr1:93719400-93727600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:93719400-93727600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:93719400-93727600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:93719400-93727600	Weak transcription	Fetal Stomach	stomach
27	chr1:93719400-93728000	Weak transcription	Left Ventricle	heart
28	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:93720400-93728200	Weak transcription	HSMM	muscle
30	chr1:93721200-93727600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:93721200-93731400	Weak transcription	NH-A	brain
32	chr1:93721400-93727600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:93724200-93727600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:93724200-93731800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:93725200-93732600	Weak transcription	NHDF-Ad	bronchial
36	chr1:93725600-93728400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:93725800-93727600	Weak transcription	Psoas Muscle	Psoas
38	chr1:93726000-93728000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:93726200-93729800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr1:93726400-93728000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:93726400-93728400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:93726400-93729800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:93726400-93730200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:93726400-93731600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:93726400-93731800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr1:93726400-93732000	Weak transcription	Right Ventricle	heart
47	chr1:93726600-93731800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr1:93726600-93731800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr1:93726800-93730000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr1:93726800-93730400	ZNF genes & repeats	Primary B cells from cord blood	blood

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