Variant report

Variant	rs2526398
Chromosome Location	chr3:50187596-50187597
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	POLR2A	chr3:50187395-50187904	HepG2	liver:	n/a	n/a
2	EP300	chr3:50187169-50187620	HepG2	liver:	n/a	n/a
3	HDAC2	chr3:50187208-50187819	HepG2	liver:	n/a	n/a
4	FOXA1	chr3:50187131-50187904	HepG2	liver:	n/a	n/a
5	MYBL2	chr3:50187172-50187945	HepG2	liver:	n/a	n/a
6	FOXA1	chr3:50187209-50187776	HepG2	liver:	n/a	n/a
7	MAZ	chr3:50187281-50187781	HepG2	liver:	n/a	chr3:50187373-50187382
8	FOXA1	chr3:50187139-50187805	HepG2	liver:	n/a	n/a
9	FOXA1	chr3:50187187-50187876	HepG2	liver:	n/a	n/a
10	EP300	chr3:50187204-50187613	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:50187395-50187870	HepG2	liver:	n/a	n/a
12	HNF4G	chr3:50187436-50187812	HepG2	liver:	n/a	chr3:50187670-50187692 chr3:50187674-50187688
13	POLR2A	chr3:50187422-50187893	HepG2	liver:	n/a	n/a
14	MAX	chr3:50187340-50188102	HepG2	liver:	n/a	chr3:50187373-50187382
15	NFIC	chr3:50187209-50187854	HepG2	liver:	n/a	n/a
16	HEY1	chr3:50187441-50187852	HepG2	liver:	n/a	n/a
17	SP1	chr3:50187128-50187850	HepG2	liver:	n/a	chr3:50187419-50187433 chr3:50187418-50187430 chr3:50187599-50187608 chr3:50187420-50187429
18	FOXA2	chr3:50187546-50187824	HepG2	liver:	n/a	n/a
19	MAFK	chr3:50187542-50187765	HepG2	liver:	n/a	n/a
20	CHD2	chr3:50187446-50187806	HepG2	liver:	n/a	n/a
21	CEBPD	chr3:50187249-50187705	HepG2	liver:	n/a	n/a
22	MYC	chr3:50187570-50187729	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50157890..50164898-chr3:50186493..50191745,15	MCF-7	breast:
2	chr3:50187119..50189930-chr3:50262235..50264960,2	MCF-7	breast:
3	chr3:50187141..50189359-chr3:50306420..50308103,2	MCF-7	breast:
4	chr3:50187263..50189349-chr5:111741686..111743310,2	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000012171	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1046956	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919418	0.85[EUR][1000 genomes]
rs12632110	0.82[EUR][1000 genomes]
rs12637671	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13059311	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064381	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067082	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs14321	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs2014004	1.00[ASN][1000 genomes]
rs2188151	0.81[AMR][1000 genomes]
rs2526384	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526387	1.00[ASN][1000 genomes]
rs2526397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624833	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624835	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2624838	0.84[EUR][1000 genomes]
rs2624841	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55924524	1.00[ASN][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62263602	1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6800021	0.82[AMR][1000 genomes]
rs6807194	0.81[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7648652	1.00[ASN][1000 genomes]
rs9858297	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
15	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2526398	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2526398	HYAL3	cis	Esophagus Muscularis	GTEx
rs2526398	RBM6	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50177200-50191800	Weak transcription	Right Ventricle	heart
2	chr3:50177600-50191000	Weak transcription	Lung	lung
3	chr3:50183600-50192000	Enhancers	Esophagus	oesophagus
4	chr3:50183800-50189800	Enhancers	Fetal Stomach	stomach
5	chr3:50184000-50187600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50184000-50187600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:50184400-50187600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:50185000-50189600	Enhancers	Fetal Lung	lung
9	chr3:50185200-50187600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:50185200-50188200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:50185600-50187600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:50185600-50187600	Weak transcription	NHEK	skin
13	chr3:50185800-50187600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:50186200-50187600	Weak transcription	Fetal Kidney	kidney
15	chr3:50186200-50188400	Weak transcription	Fetal Brain Male	brain
16	chr3:50186200-50191600	Weak transcription	Fetal Brain Female	brain
17	chr3:50186400-50187600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:50187200-50188400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:50187200-50188400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:50187200-50188800	Flanking Active TSS	HepG2	liver
21	chr3:50187200-50189600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:50187200-50189800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:50187200-50190000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:50187400-50187600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:50187400-50187800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:50187400-50188400	Enhancers	Spleen	Spleen
27	chr3:50187400-50188800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:50187400-50188800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:50187400-50188800	Enhancers	Fetal Muscle Trunk	muscle
30	chr3:50187400-50189000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr3:50187400-50189200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:50187400-50189400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:50187400-50189400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:50187400-50189400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:50187400-50189400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:50187400-50189600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:50187400-50189800	Enhancers	Placenta	Placenta
38	chr3:50187400-50190000	Enhancers	Fetal Muscle Leg	muscle
39	chr3:50187400-50190000	Enhancers	Fetal Thymus	thymus

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