Variant report

Variant	rs57785091
Chromosome Location	chr2:190539475-190539476
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	ELF1	chr2:190539007-190539594	GM12878	blood:	n/a	chr2:190539280-190539292 chr2:190539189-190539201
2	USF2	chr2:190539055-190539646	H1-hESC	embryonic stem cell:	n/a	chr2:190539209-190539225 chr2:190539312-190539328
3	RAD21	chr2:190539012-190539513	SK-N-SH_RA	brain:	n/a	chr2:190539201-190539211
4	POLR2A	chr2:190538889-190539761	GM12892	blood:	n/a	n/a
5	GABPA	chr2:190539103-190539699	A549	lung:	n/a	chr2:190539158-190539167
6	POLR2A	chr2:190538953-190539704	SK-N-SH	brain:	n/a	n/a
7	ELF1	chr2:190539115-190539998	MCF-7	breast:	n/a	chr2:190539280-190539292 chr2:190539189-190539201
8	POLR2A	chr2:190538049-190539923	GM12891	blood:	n/a	n/a
9	FOXA1	chr2:190538917-190539532	HepG2	liver:	n/a	n/a
10	ATF2	chr2:190538937-190539616	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:190539130-190539658	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:190539010-190539631	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:190539017-190539996	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:190539094-190539684	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:190538921-190539783	GM12892	blood:	n/a	n/a
16	POLR2A	chr2:190538997-190539733	IMR90	lung:	n/a	n/a
17	POLR2A	chr2:190538983-190539715	HepG2	liver:	n/a	n/a
18	SP1	chr2:190539068-190539588	GM12878	blood:	n/a	n/a
19	CHD2	chr2:190538997-190539697	GM12878	blood:	n/a	n/a
20	RFX5	chr2:190539030-190539561	GM12878	blood:	n/a	n/a
21	YY1	chr2:190539080-190539783	SK-N-SH	brain:	n/a	chr2:190539188-190539202 chr2:190539193-190539202
22	TAF1	chr2:190539046-190539675	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr2:190538569-190539948	A549	lung:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
24	E2F4	chr2:190539088-190539481	MCF10A-Er-Src	breast:	n/a	chr2:190539195-190539205
25	TCF7L2	chr2:190539255-190539735	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:190538947-190539755	GM12891	blood:	n/a	n/a
27	HDAC2	chr2:190538972-190539484	H1-hESC	embryonic stem cell:	n/a	n/a
28	PML	chr2:190538715-190539878	GM12878	blood:	n/a	n/a
29	MYBL2	chr2:190538677-190539983	HepG2	liver:	n/a	n/a
30	CHD2	chr2:190539166-190539668	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr2:190539135-190539573	GM12892	blood:	n/a	n/a
32	CTCF	chr2:190538925-190539548	H1-hESC	embryonic stem cell:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
33	TAF7	chr2:190539014-190539715	H1-hESC	embryonic stem cell:	n/a	n/a
34	NRF1	chr2:190539017-190539581	GM12878	blood:	n/a	chr2:190539158-190539167
35	NFIC	chr2:190538954-190539823	HepG2	liver:	n/a	n/a
36	CTCF	chr2:190539034-190539482	GM12892	blood:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
37	SIN3AK20	chr2:190539171-190539552	HepG2	liver:	n/a	n/a
38	TAF1	chr2:190539000-190539676	HepG2	liver:	n/a	n/a
39	REST	chr2:190539006-190539499	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr2:190539011-190539487	MCF-7	breast:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
41	MAZ	chr2:190538978-190539581	HepG2	liver:	n/a	n/a
42	ZBTB7A	chr2:190538991-190539475	HepG2	liver:	n/a	chr2:190539203-190539212
43	MAX	chr2:190538928-190539599	H1-hESC	embryonic stem cell:	n/a	n/a
44	TEAD4	chr2:190538873-190539605	HepG2	liver:	n/a	n/a
45	RAD21	chr2:190539050-190539499	GM12878	blood:	n/a	chr2:190539201-190539211
46	ZBTB33	chr2:190539185-190539588	A549	lung:	n/a	chr2:190539450-190539465
47	POU2F2	chr2:190538972-190539570	GM12891	blood:	n/a	n/a
48	MAX	chr2:190538879-190539782	SK-N-SH	brain:	n/a	n/a
49	JUND	chr2:190539002-190539866	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAFK	chr2:190539382-190539904	Hela-S3	cervix:	n/a	chr2:190539789-190539804

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:
2	chr2:190525525..190526412-chr2:190538733..190539795,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OSGEPL1-2	chr2:190538557-190539617	NONHSAT076058

Variant related genes	Relation type
ANKAR	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000138381	Chromatin interaction
ENSG00000128694	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10197551	0.89[AFR][1000 genomes]
rs10197577	0.89[AFR][1000 genomes]
rs10497706	0.92[AFR][1000 genomes]
rs13390239	0.91[AFR][1000 genomes]
rs13400261	0.84[AFR][1000 genomes]
rs13404356	0.92[AFR][1000 genomes]
rs13411095	0.87[AFR][1000 genomes]
rs13416709	0.92[AFR][1000 genomes]
rs13418043	0.91[AFR][1000 genomes]
rs13418158	0.89[AFR][1000 genomes]
rs13418434	0.92[AFR][1000 genomes]
rs13429804	0.92[AFR][1000 genomes]
rs16831975	0.89[AFR][1000 genomes]
rs2118453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742923	0.88[AFR][1000 genomes]
rs5742932	0.81[AFR][1000 genomes]
rs5742935	0.83[AFR][1000 genomes]
rs5742944	0.88[AFR][1000 genomes]
rs5742979	0.81[AFR][1000 genomes]
rs6711817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6746951	0.88[AFR][1000 genomes]
rs6760126	0.87[AFR][1000 genomes]
rs73048418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73049960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73050376	0.92[AFR][1000 genomes]
rs7560735	0.87[AFR][1000 genomes]
rs7577159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190528600-190539600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:190530000-190542800	Strong transcription	Dnd41	blood
4	chr2:190534000-190550200	Weak transcription	K562	blood
5	chr2:190538400-190540000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr2:190538600-190540000	Flanking Active TSS	GM12878-XiMat	blood
7	chr2:190538600-190540200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr2:190538600-190540200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:190538600-190540200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:190538600-190540200	Flanking Active TSS	HUVEC	blood vessel
11	chr2:190538600-190540400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:190538600-190540400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:190538800-190539800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:190538800-190539800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:190538800-190539800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr2:190538800-190539800	Flanking Active TSS	Fetal Thymus	thymus
17	chr2:190538800-190540000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:190538800-190540000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:190538800-190540000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:190538800-190540000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr2:190538800-190540000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:190538800-190540000	Active TSS	Fetal Kidney	kidney
23	chr2:190538800-190540000	Active TSS	Left Ventricle	heart
24	chr2:190538800-190540000	Flanking Active TSS	HMEC	breast
25	chr2:190538800-190540200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr2:190538800-190540200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:190538800-190540200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr2:190538800-190540200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr2:190538800-190540200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr2:190538800-190540200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:190538800-190540200	Active TSS	Psoas Muscle	Psoas
32	chr2:190538800-190540200	Active TSS	Right Atrium	heart
33	chr2:190538800-190540400	Active TSS	NHDF-Ad	bronchial
34	chr2:190539000-190539600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:190539000-190539600	Active TSS	Primary T cells from cord blood	blood
36	chr2:190539000-190539600	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr2:190539000-190539600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr2:190539000-190539600	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr2:190539000-190539600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:190539000-190539600	Active TSS	Fetal Heart	heart
41	chr2:190539000-190539600	Active TSS	Fetal Lung	lung
42	chr2:190539000-190539600	Active TSS	Placenta	Placenta
43	chr2:190539000-190539600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr2:190539000-190539600	Active TSS	Rectal Smooth Muscle	rectum
45	chr2:190539000-190539600	Active TSS	HSMMtube	muscle
46	chr2:190539000-190539600	Active TSS	Osteobl	bone
47	chr2:190539000-190539800	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:190539000-190539800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:190539000-190539800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:190539000-190539800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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