Variant report

Variant	rs712072
Chromosome Location	chr1:224716938-224716939
allele	C/G
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	TCF12	chr1:224716406-224717291	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:224716540-224717065	HUVEC	blood vessel:	n/a	n/a
3	RCOR1	chr1:224716604-224717017	K562	blood:	n/a	n/a
4	JUN	chr1:224716619-224717033	K562	blood:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
5	NFIC	chr1:224716477-224717292	SK-N-SH	brain:	n/a	n/a
6	SETDB1	chr1:224716640-224717091	U2OS	brain:	n/a	n/a
7	JUN	chr1:224716659-224717007	K562	blood:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
8	USF1	chr1:224716549-224717043	SK-N-SH	brain:	n/a	chr1:224716830-224716841
9	USF1	chr1:224716546-224717018	HCT-116	colon:	n/a	chr1:224716830-224716841
10	JUN	chr1:224716734-224717028	HepG2	liver:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
11	REST	chr1:224716614-224717052	PFSK-1	brain:	n/a	chr1:224716783-224716796 chr1:224716786-224716799
12	ATF1	chr1:224716670-224716955	K562	blood:	n/a	n/a
13	EP300	chr1:224716435-224717304	SK-N-SH	brain:	n/a	chr1:224716820-224716829
14	ELF1	chr1:224716570-224717007	K562	blood:	n/a	n/a
15	EP300	chr1:224716647-224716990	K562	blood:	n/a	chr1:224716820-224716829
16	MAX	chr1:224716693-224716953	K562	blood:	n/a	n/a
17	NR2F2	chr1:224716617-224716957	K562	blood:	n/a	n/a
18	POLR2A	chr1:224716651-224717001	PFSK-1	brain:	n/a	n/a
19	JUND	chr1:224716565-224717046	K562	blood:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
20	FOS	chr1:224716669-224717011	MCF10A-Er-Src	breast:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
21	STAT3	chr1:224716803-224717050	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr1:224716418-224717369	SK-N-SH	brain:	n/a	n/a
23	GATA2	chr1:224716620-224717088	HUVEC	blood vessel:	n/a	n/a
24	FOSL2	chr1:224716580-224716958	HepG2	liver:	n/a	chr1:224716818-224716829 chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
25	JUND	chr1:224716673-224716987	HepG2	liver:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
26	GATA3	chr1:224716688-224717076	MCF-7	breast:	n/a	n/a
27	TEAD4	chr1:224716615-224717031	K562	blood:	n/a	n/a
28	USF1	chr1:224716595-224717019	H1-hESC	embryonic stem cell:	n/a	chr1:224716830-224716841
29	USF1	chr1:224716577-224716982	SK-N-SH_RA	brain:	n/a	chr1:224716830-224716841
30	POLR2A	chr1:224716613-224717032	SK-N-SH	brain:	n/a	n/a
31	FOSL2	chr1:224716504-224717187	SK-N-SH	brain:	n/a	chr1:224716818-224716829 chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
32	JUND	chr1:224716500-224717081	SK-N-SH	brain:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
33	GATA3	chr1:224716481-224717312	SK-N-SH	brain:	n/a	n/a
34	JUN	chr1:224716630-224717005	K562	blood:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
35	FOSL2	chr1:224716612-224716976	HepG2	liver:	n/a	chr1:224716818-224716829 chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
36	BHLHE40	chr1:224716707-224716939	K562	blood:	n/a	n/a
37	KAP1	chr1:224716551-224717061	U2OS	brain:	n/a	n/a
38	FOXA2	chr1:224716784-224716942	HepG2	liver:	n/a	n/a
39	RCOR1	chr1:224716677-224716939	K562	blood:	n/a	n/a
40	ZNF263	chr1:224716538-224717038	HEK293-T-REx	kidney:	n/a	n/a
41	JUN	chr1:224716277-224718250	K562	blood:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828
42	REST	chr1:224716674-224716945	SK-N-SH	brain:	n/a	chr1:224716783-224716796 chr1:224716786-224716799
43	GABPA	chr1:224716627-224716992	MCF-7	breast:	n/a	n/a
44	JUND	chr1:224716675-224716998	H1-hESC	embryonic stem cell:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
45	FOS	chr1:224716605-224717049	HUVEC	blood vessel:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
46	ATF3	chr1:224716627-224716949	K562	blood:	n/a	n/a
47	FOS	chr1:224716654-224717008	MCF10A-Er-Src	breast:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
48	CBX3	chr1:224716623-224716960	K562	blood:	n/a	n/a
49	JUND	chr1:224716278-224717206	SK-N-SH	brain:	n/a	chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716819-224716830 chr1:224716817-224716828
50	FOSL2	chr1:224716639-224717035	MCF-7	breast:	n/a	chr1:224716818-224716829 chr1:224716819-224716831 chr1:224716820-224716829 chr1:224716822-224716829 chr1:224716817-224716828

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224716924-224717122	NONHSAT009812
2	lnc-CNIH3-2	chr1:224716925-224717122	NONHSAT009813

Variant related genes	Relation type
CNIH3	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10799582	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916635	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916636	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916637	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916638	0.85[EUR][1000 genomes]
rs10916639	0.92[EUR][1000 genomes]
rs10916640	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033478	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12043625	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12057775	0.91[CEU][hapmap];0.93[CHB][hapmap];0.93[EUR][1000 genomes]
rs12062991	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12068420	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12072482	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317810	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499283	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16849369	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2050625	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2794804	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654047	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61825839	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61825840	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825841	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6656824	0.95[EUR][1000 genomes]
rs698277	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs698280	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712070	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712073	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712074	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712075	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712076	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712082	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712084	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712085	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712087	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712092	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541415	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs791391	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs791393	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs791508	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs791509	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791510	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs791511	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791512	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880368	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs983948	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs985301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989755	0.94[EUR][1000 genomes];0.87[ASN][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712072	LEFTY1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224711200-224720400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:224712000-224730800	Weak transcription	Spleen	Spleen
5	chr1:224713400-224721400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:224716200-224718000	Enhancers	HUVEC	blood vessel
7	chr1:224716400-224717200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:224716400-224717800	Enhancers	NHDF-Ad	bronchial
9	chr1:224716400-224717800	Enhancers	Osteobl	bone
10	chr1:224716400-224718000	Enhancers	HMEC	breast
11	chr1:224716400-224718000	Enhancers	NHLF	lung
12	chr1:224716400-224718200	Enhancers	HSMM	muscle
13	chr1:224716600-224717000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:224716600-224717000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:224716600-224717000	Enhancers	Brain Angular Gyrus	brain
16	chr1:224716600-224717000	Enhancers	Fetal Lung	lung
17	chr1:224716600-224717000	Enhancers	Fetal Muscle Leg	muscle
18	chr1:224716600-224717000	Enhancers	Fetal Stomach	stomach
19	chr1:224716600-224717200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:224716600-224717200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr1:224716600-224717200	Enhancers	A549	lung
22	chr1:224716600-224717200	Enhancers	Hela-S3	cervix
23	chr1:224716600-224717400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:224716600-224717400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:224716600-224717400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:224716600-224717400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:224716600-224717400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:224716600-224717400	Enhancers	Lung	lung
29	chr1:224716600-224717600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:224716600-224717600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:224716600-224717600	Enhancers	NHEK	skin
32	chr1:224716600-224717800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:224716600-224717800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:224716600-224717800	Enhancers	Dnd41	blood
35	chr1:224716600-224717800	Enhancers	HSMMtube	muscle
36	chr1:224716600-224717800	Enhancers	NH-A	brain
37	chr1:224716600-224718000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:224716600-224718000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:224716600-224718000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:224716600-224718000	Enhancers	Pancreas	Pancrea
41	chr1:224716800-224717000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:224716800-224717000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:224716800-224717000	Enhancers	Fetal Brain Male	brain
44	chr1:224716800-224717200	Enhancers	K562	blood
45	chr1:224716800-224717800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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