Variant report

Variant	rs9789678
Chromosome Location	chr2:208899477-208899478
allele	A/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	SETDB1	chr2:208898789-208899766	U2OS	brain:	n/a	n/a
2	POLR2A	chr2:208899293-208899714	K562	blood:	n/a	n/a
3	KAP1	chr2:208898747-208899550	HEK293	kidney:	n/a	n/a
4	ARID3A	chr2:208898525-208899631	HepG2	liver:	n/a	n/a
5	JUND	chr2:208898449-208899557	HepG2	liver:	n/a	chr2:208898984-208898995

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208899128..208901283-chr2:208902115..208904520,2	K562	blood:
2	chr2:208888946..208890856-chr2:208898000..208900571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185078	TF binding region
ENSG00000178385	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10192065	0.89[CEU][hapmap]
rs10193505	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10193523	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10196408	0.90[EUR][1000 genomes]
rs10198217	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10497891	0.89[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs10497892	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10497894	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10804164	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10932218	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10932220	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10932221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10932223	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10932225	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10932226	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10932227	0.87[ASN][1000 genomes]
rs10932228	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11676872	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11679374	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687058	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11687255	0.89[ASN][1000 genomes]
rs11688041	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11688936	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11694308	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11891423	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11893393	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12465154	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12469400	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612391	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12694097	0.85[EUR][1000 genomes]
rs13002375	0.80[EUR][1000 genomes]
rs13002973	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13005382	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13006024	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13018735	0.86[ASN][1000 genomes]
rs13387203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13420900	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13421034	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466185	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466186	0.88[ASN][1000 genomes]
rs1545503	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16840362	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16840390	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16840392	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17598650	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17640827	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs17641035	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1812697	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1965865	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044971	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2084870	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2084871	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2100348	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2100349	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2100351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2123294	0.95[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2362782	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2362783	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2362786	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2362788	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2362789	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2885599	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2885600	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34025579	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34335027	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34354040	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35594487	0.80[EUR][1000 genomes]
rs35687108	0.84[EUR][1000 genomes]
rs35726860	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35783183	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35968595	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3795911	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3795912	1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4021953	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4441448	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4507086	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4673377	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4675722	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4675723	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4675724	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4675725	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4675726	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55883450	0.89[ASN][1000 genomes]
rs56007263	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56340702	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56812613	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60679550	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6435403	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6435404	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6712527	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6718363	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6718487	0.83[ASN][1000 genomes]
rs6723557	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6733857	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67351199	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6741366	0.95[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67417299	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6757323	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6757327	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7355275	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7424035	0.90[ASN][1000 genomes]
rs7559294	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7559399	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560222	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562306	0.82[EUR][1000 genomes]
rs7570588	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7573629	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585863	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7592525	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7595734	1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7595823	0.81[CEU][hapmap]
rs7599531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604044	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608939	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7609209	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7609428	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs764299	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs896636	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs921554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921555	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930746	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs966317	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9679132	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9789442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9789446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9789586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208891000-208904200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:208891000-208905400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:208896600-208901000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:208896600-208907600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:208898000-208899800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:208898400-208899600	Enhancers	Hela-S3	cervix
7	chr2:208899000-208912000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:208899200-208901200	Weak transcription	Placenta	Placenta
9	chr2:208899400-208900200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:208899400-208901200	Enhancers	HepG2	liver

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