Variant report

Variant	rs7513705
Chromosome Location	chr1:93666349-93666350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr1:93666077-93666792	HepG2	liver:	n/a	chr1:93666466-93666482 chr1:93666470-93666479 chr1:93666466-93666482 chr1:93666538-93666548 chr1:93666467-93666481 chr1:93666470-93666480 chr1:93666469-93666478
2	ZEB1	chr1:93666201-93666701	HepG2	liver:	n/a	n/a
3	TEAD4	chr1:93665785-93666815	HepG2	liver:	n/a	n/a
4	MYBL2	chr1:93666171-93666789	HepG2	liver:	n/a	n/a
5	EP300	chr1:93666165-93666775	HepG2	liver:	n/a	n/a
6	BHLHE40	chr1:93666318-93666562	HepG2	liver:	n/a	n/a
7	FOXA1	chr1:93666262-93666740	HepG2	liver:	n/a	chr1:93666439-93666451
8	EP300	chr1:93666304-93666709	HepG2	liver:	n/a	n/a
9	FOXA2	chr1:93666228-93666720	HepG2	liver:	n/a	chr1:93666439-93666451
10	FOXA1	chr1:93666206-93666750	HepG2	liver:	n/a	chr1:93666439-93666451
11	NFIC	chr1:93666289-93666721	HepG2	liver:	n/a	n/a
12	FOXA1	chr1:93666175-93666754	HepG2	liver:	n/a	chr1:93666439-93666451
13	NFIC	chr1:93666214-93666724	HepG2	liver:	n/a	n/a
14	MYBL2	chr1:93666233-93666665	HepG2	liver:	n/a	n/a
15	SP1	chr1:93666258-93666674	HepG2	liver:	n/a	n/a
16	FOXA2	chr1:93665946-93666952	HepG2	liver:	n/a	chr1:93666439-93666451
17	HNF4A	chr1:93666331-93666641	HepG2	liver:	n/a	chr1:93666536-93666544

No.	Distal block	Cell Line	Cell type
1	chr1:93665864..93667749-chr1:93671794..93674252,2	K562	blood:
2	chr1:93646277..93649734-chr1:93664673..93670683,6	K562	blood:
3	chr1:93645225..93647960-chr1:93665324..93667847,2	MCF-7	breast:

Variant related genes	Relation type
CCDC18	TF binding region
ENSG00000225297	TF binding region
ENSG00000122483	Chromatin interaction
ENSG00000117500	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1000607	0.86[EUR][1000 genomes]
rs1010476	0.86[CHB][hapmap]
rs1057257	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060622	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782955	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782959	0.81[CHB][hapmap]
rs10874759	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874762	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874764	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874772	0.86[EUR][1000 genomes]
rs10874773	0.86[EUR][1000 genomes]
rs11164870	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs11164876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164880	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164881	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164902	0.86[EUR][1000 genomes]
rs11164908	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12030549	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12030843	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12033147	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12038699	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12044557	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12044657	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044883	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs12062154	0.84[YRI][hapmap]
rs12118230	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12118262	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124011	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128131	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12130734	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133576	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs12139009	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12406245	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs12563120	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1335679	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1426318	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs1474927	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs1535699	0.85[EUR][1000 genomes]
rs1537758	1.00[ASN][1000 genomes]
rs1559828	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs1572343	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1856027	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs1932314	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1967721	0.91[ASN][1000 genomes]
rs2031225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs2031226	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs2152358	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255722	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2281524	0.86[CHB][hapmap]
rs2295423	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2295424	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2296558	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs2297707	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391254	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs2484486	0.85[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2749732	0.81[CHB][hapmap]
rs2765545	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2783489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2783490	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2783495	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2783499	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2783500	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2783501	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2783504	0.88[ASN][1000 genomes]
rs2815415	0.88[ASN][1000 genomes]
rs2815429	0.81[CHB][hapmap]
rs35940311	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754186	0.95[CHB][hapmap]
rs3767964	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs3904665	0.93[JPT][hapmap]
rs3904666	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs4000699	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs4240966	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs4484937	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4847235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847240	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs4847398	0.81[EUR][1000 genomes]
rs4847399	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs4847401	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4847402	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs4847410	0.85[EUR][1000 genomes]
rs531358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531514	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs535760	0.89[EUR][1000 genomes]
rs555161	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569414	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs602204	0.89[EUR][1000 genomes]
rs612037	0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61799470	0.80[ASN][1000 genomes]
rs61799471	0.86[ASN][1000 genomes]
rs61799496	0.86[ASN][1000 genomes]
rs622608	0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs624131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627779	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs637646	0.95[CHB][hapmap];0.90[EUR][1000 genomes]
rs6541349	0.85[CHB][hapmap]
rs6541401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes]
rs6541404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes]
rs6680107	0.86[EUR][1000 genomes]
rs6682670	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6688230	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs682514	0.88[EUR][1000 genomes]
rs687394	0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs693737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes]
rs7512911	0.90[EUR][1000 genomes]
rs7517363	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7524964	0.85[EUR][1000 genomes]
rs7525248	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs7526112	0.81[EUR][1000 genomes]
rs7532195	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532549	0.83[EUR][1000 genomes]
rs7535628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537403	0.86[EUR][1000 genomes]
rs7539307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540025	0.86[EUR][1000 genomes]
rs7541304	0.86[EUR][1000 genomes]
rs7541687	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547244	0.86[EUR][1000 genomes]
rs7551485	0.86[EUR][1000 genomes]
rs7553465	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7553916	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs771481	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs797661	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs797666	0.89[EUR][1000 genomes]
rs797668	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs797671	0.87[EUR][1000 genomes]
rs797672	0.91[EUR][1000 genomes]
rs797675	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs797676	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs797680	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs797681	0.89[EUR][1000 genomes]
rs810027	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs942196	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs9432453	0.86[EUR][1000 genomes]
rs9432465	0.84[EUR][1000 genomes]
rs9432681	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7513705	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs7513705	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs7513705	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs7513705	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7513705	RP4-717I23.3	cis	Artery Tibial	GTEx
rs7513705	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs7513705	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs7513705	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs7513705	RP4-717I23.3	cis	Thyroid	GTEx
rs7513705	RP4-717I23.3	cis	lung	GTEx
rs7513705	DR1	cis	multi-tissue	Pritchard
rs7513705	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs7513705	DR1	cis	Adipose Subcutaneous	GTEx
rs7513705	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs7513705	RP4-717I23.3	cis	Whole Blood	GTEx
rs7513705	RP4-717I23.3	cis	Artery Aorta	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93647000-93756400	Weak transcription	Gastric	stomach
4	chr1:93647200-93667600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:93647200-93667600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:93647200-93668200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:93647200-93681200	Weak transcription	HUVEC	blood vessel
8	chr1:93647200-93684400	Weak transcription	NH-A	brain
9	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:93647400-93667400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:93647600-93670400	Weak transcription	Liver	Liver
14	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:93647800-93667800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:93648400-93672200	Weak transcription	A549	lung
17	chr1:93649000-93684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:93651000-93684800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:93651400-93678000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
21	chr1:93654600-93708000	Weak transcription	Ovary	ovary
22	chr1:93655200-93674000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:93656400-93668000	Weak transcription	Fetal Lung	lung
24	chr1:93656400-93686200	Weak transcription	Aorta	Aorta
25	chr1:93656800-93669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:93657000-93682000	Strong transcription	Dnd41	blood
27	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
28	chr1:93658400-93666800	Weak transcription	Brain Germinal Matrix	brain
29	chr1:93658600-93667800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:93658600-93667800	Weak transcription	K562	blood
31	chr1:93658600-93668000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:93658600-93684800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:93658800-93684400	Weak transcription	Osteobl	bone
34	chr1:93660600-93666600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:93660600-93671000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:93660600-93705200	Weak transcription	Lung	lung
37	chr1:93660800-93667400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:93660800-93669400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:93660800-93685000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:93661000-93674200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:93661200-93667400	Weak transcription	NHDF-Ad	bronchial
42	chr1:93661200-93667800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:93661400-93667400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:93661800-93702800	Weak transcription	Fetal Heart	heart
46	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
47	chr1:93662800-93667800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:93663000-93673400	Weak transcription	Hela-S3	cervix
49	chr1:93663400-93669800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:93663600-93667000	Strong transcription	Fetal Thymus	thymus

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