Variant report

Variant	rs2890339
Chromosome Location	chr1:247298975-247298976
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	chr1:247267372..247270234-chr1:247298107..247300511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188295	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10465609	1.00[ASN][1000 genomes]
rs10465619	1.00[ASN][1000 genomes]
rs10493861	0.97[ASN][1000 genomes]
rs10754537	0.91[ASN][1000 genomes]
rs10802471	0.98[ASN][1000 genomes]
rs10924924	0.80[ASN][1000 genomes]
rs10924927	1.00[ASN][1000 genomes]
rs10924928	1.00[ASN][1000 genomes]
rs11801681	0.82[ASN][1000 genomes]
rs12058648	0.80[ASN][1000 genomes]
rs12076177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076273	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093759	0.98[ASN][1000 genomes]
rs12120049	0.80[ASN][1000 genomes]
rs12133112	0.94[ASN][1000 genomes]
rs12141126	0.91[ASN][1000 genomes]
rs12144854	0.82[ASN][1000 genomes]
rs16846292	0.98[ASN][1000 genomes]
rs3844079	0.97[ASN][1000 genomes]
rs3844080	0.95[ASN][1000 genomes]
rs4105113	0.97[ASN][1000 genomes]
rs4925701	0.80[ASN][1000 genomes]
rs4925702	0.82[ASN][1000 genomes]
rs4925703	0.80[ASN][1000 genomes]
rs4925704	0.82[ASN][1000 genomes]
rs4925711	0.82[ASN][1000 genomes]
rs4925715	0.82[ASN][1000 genomes]
rs6659254	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675536	0.91[ASN][1000 genomes]
rs6688822	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700358	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700824	0.82[ASN][1000 genomes]
rs7521596	0.97[ASN][1000 genomes]
rs7531763	0.95[ASN][1000 genomes]
rs9793102	0.91[ASN][1000 genomes]
rs9803828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9803983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
17	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
19	esv1830156	chr1:247278707-247319489	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
20	nsv873432	chr1:247278707-247334323	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
21	nsv873433	chr1:247278707-247360368	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
22	nsv549567	chr1:247279802-247306833	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
23	nsv1005008	chr1:247285853-247339833	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
24	nsv535423	chr1:247285853-247339833	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
25	esv1807956	chr1:247292244-247305873	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
26	esv1814795	chr1:247292244-247305873	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
27	esv1806065	chr1:247292296-247305873	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
28	esv3452798	chr1:247296800-247301794	ZNF genes & repeats Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
29	esv3452799	chr1:247296800-247301794	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2890339	ZNF124	Cis_1M	lymphoblastoid	RTeQTL
rs2890339	ZNF124	cis	Skin Sun Exposed Lower leg	GTEx
rs2890339	ZNF124	cis	lung	GTEx
rs2890339	ZNF124	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247293400-247300600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:247295200-247307400	Weak transcription	Right Ventricle	heart
3	chr1:247295400-247299400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:247295600-247302000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:247295600-247303800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:247295600-247304400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:247297400-247300000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:247298200-247302400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:247298800-247299600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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