Variant report

Variant	rs2526389
Chromosome Location	chr3:50192826-50192827
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	MAX	chr3:50192284-50192911	ECC-1	luminal epithelium:	n/a	n/a
2	REST	chr3:50191706-50193577	H1-neurons	neurons:	n/a	chr3:50192632-50192645 chr3:50193092-50193102 chr3:50192628-50192648 chr3:50193114-50193124 chr3:50192001-50192014 chr3:50192628-50192648
3	CREB1	chr3:50192309-50193270	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:50191801-50192942	MCF-7	breast:	n/a	n/a
5	GABPA	chr3:50192430-50193104	H1-hESC	embryonic stem cell:	n/a	chr3:50192889-50192898
6	ELF1	chr3:50192664-50192881	K562	blood:	n/a	chr3:50192841-50192853 chr3:50192842-50192854
7	SIN3AK20	chr3:50192385-50193019	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr3:50192780-50192930	GM12867	blood:	n/a	n/a
9	RAD21	chr3:50192458-50192910	HepG2	liver:	n/a	chr3:50192717-50192727
10	GABPA	chr3:50192484-50193046	H1-hESC	embryonic stem cell:	n/a	chr3:50192889-50192898
11	RAD21	chr3:50192496-50192894	IMR90	lung:	n/a	chr3:50192717-50192727
12	RAD21	chr3:50192578-50192835	A549	lung:	n/a	chr3:50192717-50192727
13	CHD1	chr3:50192283-50194228	IMR90	lung:	n/a	n/a
14	MAZ	chr3:50192468-50192846	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr3:50192541-50192860	K562	blood:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
16	CTCF	chr3:50192521-50192946	H1-hESC	embryonic stem cell:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
17	RAD21	chr3:50192447-50192984	ECC-1	luminal epithelium:	n/a	chr3:50192717-50192727
18	UBTF	chr3:50192398-50193168	K562	blood:	n/a	n/a
19	MAX	chr3:50192379-50192839	K562	blood:	n/a	n/a
20	POLR2A	chr3:50192362-50192958	HepG2	liver:	n/a	n/a
21	CCNT2	chr3:50192446-50193005	K562	blood:	n/a	n/a
22	POLR2A	chr3:50192125-50192837	MCF-7	breast:	n/a	n/a
23	RAD21	chr3:50192405-50192978	HepG2	liver:	n/a	chr3:50192717-50192727
24	POLR2A	chr3:50192131-50192922	MCF-7	breast:	n/a	n/a
25	POLR2A	chr3:50191934-50192829	H1-neurons	neurons:	n/a	n/a
26	SMARCB1	chr3:50192068-50193631	Hela-S3	cervix:	n/a	n/a
27	TFAP2A	chr3:50192788-50193770	Hela-S3	cervix:	n/a	chr3:50192904-50192912 chr3:50192904-50192912 chr3:50193112-50193124 chr3:50192904-50192912
28	POLR2A	chr3:50192203-50192912	HUVEC	blood vessel:	n/a	n/a
29	RAD21	chr3:50192561-50192863	Hela-S3	cervix:	n/a	chr3:50192717-50192727
30	CTCF	chr3:50192680-50192830	Caco-2	colon:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
31	HA-E2F1	chr3:50192367-50193025	Hela-S3	cervix:	n/a	n/a
32	ZBTB7A	chr3:50192379-50193241	K562	blood:	n/a	chr3:50192719-50192728 chr3:50193047-50193056
33	POLR2A	chr3:50192321-50192907	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr3:50192615-50192896	K562	blood:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
35	ZBTB7A	chr3:50192488-50193851	ECC-1	luminal epithelium:	n/a	chr3:50193798-50193806 chr3:50192719-50192728 chr3:50193047-50193056
36	CTCF	chr3:50192590-50192899	A549	lung:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
37	E2F6	chr3:50192453-50193226	K562	blood:	n/a	n/a
38	POLR2A	chr3:50192198-50195021	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr3:50192408-50192948	PANC-1	pancreas:	n/a	n/a
40	CTCF	chr3:50192510-50192832	HepG2	liver:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
41	CTCF	chr3:50192700-50192850	HepG2	liver:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
42	MXI1	chr3:50192401-50192902	IMR90	lung:	n/a	n/a
43	RAD21	chr3:50192423-50193136	SK-N-SH	brain:	n/a	chr3:50192717-50192727
44	CTCF	chr3:50192506-50192907	IMR90	lung:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
45	CTCF	chr3:50192680-50192830	AG09319	gingival:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
46	UBTF	chr3:50192438-50192988	K562	blood:	n/a	n/a
47	SMC3	chr3:50191268-50193403	SK-N-SH	brain:	n/a	chr3:50191660-50191668 chr3:50192013-50192023 chr3:50192717-50192727 chr3:50192013-50192027
48	CTCF	chr3:50192417-50192938	A549	lung:	n/a	chr3:50192716-50192726 chr3:50192714-50192727
49	ZBTB7A	chr3:50192522-50192858	HepG2	liver:	n/a	chr3:50192719-50192728
50	HDAC2	chr3:50192363-50193114	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50191641..50194297-chr3:50220054..50223610,4	MCF-7	breast:
2	chr3:50190470..50194491-chr3:50196225..50201802,7	K562	blood:
3	chr3:50191627..50193691-chr3:50209687..50211278,2	MCF-7	breast:
4	chr3:50192650..50196663-chr3:50219720..50222472,4	MCF-7	breast:
5	chr3:50191338..50193199-chr3:50263040..50265048,2	MCF-7	breast:
6	chr3:50192501..50194771-chr3:50274192..50275707,2	MCF-7	breast:
7	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000207922	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1005678	0.83[EUR][1000 genomes]
rs2188151	0.89[EUR][1000 genomes]
rs2518795	0.90[EUR][1000 genomes]
rs2518796	0.89[EUR][1000 genomes]
rs2624839	0.83[EUR][1000 genomes]
rs6800021	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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
20	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
21	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
22	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS 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	53 gene(s)	inside rSNPs	diseases
23	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh 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
24	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
25	esv3323037	chr3:50190548-50194846	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
26	esv3356010	chr3:50191398-50194246	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2526389	RBM6	cis	Artery Tibial	GTEx
rs2526389	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50189600-50193000	Weak transcription	Fetal Lung	lung
2	chr3:50190000-50193000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:50191600-50193200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr3:50191600-50193400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:50191800-50193000	Active TSS	Brain Anterior Caudate	brain
6	chr3:50191800-50193200	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:50191800-50193400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:50191800-50193400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:50191800-50193400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:50191800-50193400	Active TSS	Fetal Brain Female	brain
11	chr3:50191800-50193400	Active TSS	Hela-S3	cervix
12	chr3:50191800-50194400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50192000-50193000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:50192000-50193000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:50192000-50193000	Weak transcription	Fetal Heart	heart
16	chr3:50192000-50193000	Active TSS	HSMMtube	muscle
17	chr3:50192000-50193200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:50192000-50193200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:50192000-50193200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:50192000-50193200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr3:50192000-50193200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:50192000-50193200	Weak transcription	Fetal Brain Male	brain
23	chr3:50192000-50193200	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr3:50192000-50193200	Active TSS	A549	lung
25	chr3:50192000-50193200	Bivalent/Poised TSS	HSMM	muscle
26	chr3:50192000-50193400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr3:50192000-50193400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:50192000-50193400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:50192000-50193400	Active TSS	K562	blood
30	chr3:50192000-50193600	Active TSS	Aorta	Aorta
31	chr3:50192000-50193600	Active TSS	Small Intestine	intestine
32	chr3:50192000-50193800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr3:50192000-50194400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:50192000-50194400	Active TSS	Psoas Muscle	Psoas
35	chr3:50192000-50194800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:50192000-50194800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:50192000-50194800	Active TSS	Gastric	stomach
38	chr3:50192000-50194800	Active TSS	Left Ventricle	heart
39	chr3:50192000-50194800	Active TSS	Right Atrium	heart
40	chr3:50192200-50193000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:50192200-50193000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:50192200-50193000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
43	chr3:50192200-50193000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:50192200-50193000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr3:50192200-50193000	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr3:50192200-50193000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:50192200-50193000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:50192200-50193000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:50192200-50193000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:50192200-50193000	Active TSS	Adipose Nuclei	Adipose

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