Variant report

Variant	rs12698579
Chromosome Location	chr7:66843712-66843713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66842963..66843775-chr7:69626464..69627151,2	K562	blood:
2	chr7:66842895..66843844-chr7:69506111..69506611,2	K562	blood:
3	chr7:66842914..66843798-chr7:69396772..69397448,2	MCF-7	breast:
4	chr7:66843189..66843805-chr7:66948880..66949474,3	MCF-7	breast:
5	chr7:66843281..66844030-chr7:69396720..69397270,2	MCF-7	breast:
6	chr7:66843114..66843901-chr7:67089975..67090726,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10224468	0.82[EUR][1000 genomes]
rs10249620	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950071	0.81[EUR][1000 genomes]
rs11765153	0.85[EUR][1000 genomes]
rs11765818	0.86[EUR][1000 genomes]
rs11767326	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970911	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976633	0.81[EUR][1000 genomes]
rs11983916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12112805	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698581	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12698582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12698583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12698586	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1989425	0.87[EUR][1000 genomes]
rs2017343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2017374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421292	0.93[ASN][1000 genomes]
rs36108509	0.84[EUR][1000 genomes]
rs4717375	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4717378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718539	0.87[EUR][1000 genomes]
rs4718544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62467569	0.85[EUR][1000 genomes]
rs62467571	0.86[EUR][1000 genomes]
rs6460340	0.87[EUR][1000 genomes]
rs6947353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6958460	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6963760	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6967594	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7788614	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796287	0.88[AFR][1000 genomes]
rs985435	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031560	chr7:66805244-66846663	Enhancers Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022779	chr7:66805244-66849392	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1031147	chr7:66811313-66922350	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1025049	chr7:66823977-66906930	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3374929	chr7:66843317-66848115	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12698579	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs12698579	STAG3L4	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66842800-66844000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr7:66842800-66844000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr7:66842800-66844200	Enhancers	Fetal Muscle Leg	muscle
4	chr7:66843000-66843800	Enhancers	Brain Hippocampus Middle	brain
5	chr7:66843000-66843800	Enhancers	Spleen	Spleen
6	chr7:66843000-66844000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:66843000-66844000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:66843000-66844000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:66843000-66847200	Enhancers	Fetal Stomach	stomach
10	chr7:66843200-66843800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:66843200-66843800	Enhancers	Brain Anterior Caudate	brain
12	chr7:66843200-66843800	Enhancers	Brain Cingulate Gyrus	brain
13	chr7:66843200-66843800	Enhancers	Brain Germinal Matrix	brain
14	chr7:66843200-66843800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr7:66843200-66843800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr7:66843200-66844000	Enhancers	Colon Smooth Muscle	Colon
17	chr7:66843200-66844000	Enhancers	Ovary	ovary
18	chr7:66843400-66843800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr7:66843400-66843800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:66843400-66843800	Enhancers	Fetal Lung	lung
21	chr7:66843400-66843800	Enhancers	Stomach Smooth Muscle	stomach
22	chr7:66843600-66843800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:66843600-66843800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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