Variant report

Variant	rs11880124
Chromosome Location	chr19:42683791-42683792
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	POLR2A	chr19:42683501-42684047	H1-neurons	neurons:	n/a	n/a
2	SIN3A	chr19:42683467-42683804	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:42682982-42683887	SK-N-SH	brain:	n/a	chr19:42683575-42683588 chr19:42683573-42683591
4	CTCF	chr19:42679442-42684445	A549	lung:	n/a	chr19:42681436-42681449 chr19:42683575-42683588 chr19:42683573-42683591
5	RAD21	chr19:42683382-42683801	H1-hESC	embryonic stem cell:	n/a	chr19:42683575-42683589 chr19:42683575-42683585 chr19:42683574-42683587 chr19:42683571-42683590
6	MAX	chr19:42683354-42683942	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr19:42683416-42683827	HEK293-T-REx	kidney:	n/a	chr19:42683491-42683500 chr19:42683489-42683510
8	POLR2A	chr19:42683596-42684012	H1-neurons	neurons:	n/a	n/a
9	MAX	chr19:42683565-42683894	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr19:42683619-42683796	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr19:42683276-42683841	H1-hESC	embryonic stem cell:	n/a	chr19:42683575-42683589 chr19:42683575-42683585 chr19:42683574-42683587 chr19:42683571-42683590 chr19:42683324-42683333
12	CTCF	chr19:42683241-42683848	K562	blood:	n/a	chr19:42683575-42683588 chr19:42683573-42683591
13	CTCF	chr19:42683780-42683930	HRPEpiC	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42659646..42661683-chr19:42683231..42685564,2	K562	blood:
2	chr19:42675536..42679754-chr19:42681291..42684453,3	MCF-7	breast:
3	chr19:42679426..42681337-chr19:42681820..42684730,2	K562	blood:
4	chr19:42682574..42684413-chr19:42921728..42924640,2	K562	blood:
5	chr19:42612411..42613357-chr19:42683156..42684169,3	K562	blood:
6	chr19:42585189..42586779-chr19:42682804..42685130,2	K562	blood:
7	chr19:42637011..42637844-chr19:42683261..42684041,2	MCF-7	breast:

Variant related genes	Relation type
POU2F2	TF binding region
ENSG00000028277	Chromatin interaction
ENSG00000266226	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10407506	0.86[CHD][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs10410185	0.82[CHB][hapmap]
rs10410198	0.82[CHB][hapmap]
rs10410698	0.82[CHB][hapmap]
rs10500285	0.86[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs11878620	0.86[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11883412	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1206009	0.82[CHB][hapmap]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs12232804	0.82[ASN][1000 genomes]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.85[CHD][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs16975684	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17270169	0.85[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs17342284	0.85[CHB][hapmap]
rs17750207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217342	0.82[TSI][hapmap]
rs2267630	0.82[CHB][hapmap]
rs2302485	0.86[GIH][hapmap]
rs2303652	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2537697	0.82[CHB][hapmap]
rs2615614	0.82[CHB][hapmap]
rs28621009	0.82[CHB][hapmap]
rs3745231	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3745233	0.81[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3810148	0.82[CHB][hapmap]
rs3810151	1.00[CHB][hapmap]
rs3826705	0.85[CHD][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs4141062	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs443239	0.86[CHD][hapmap];0.91[TSI][hapmap]
rs454150	0.85[CHD][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap]
rs4803520	0.91[TSI][hapmap]
rs59099214	0.82[EUR][1000 genomes]
rs62119628	0.82[ASN][1000 genomes]
rs7248379	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251466	0.86[CHD][hapmap];0.91[TSI][hapmap]
rs73932877	1.00[ASN][1000 genomes]
rs741070	0.82[CHB][hapmap]
rs8108096	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8182491	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs851296	0.82[CHB][hapmap]
rs899661	0.91[TSI][hapmap]
rs9636121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription 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
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers 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	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42681200-42684800	Bivalent Enhancer	Fetal Thymus	thymus
2	chr19:42681800-42684200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
3	chr19:42681800-42684800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr19:42681800-42686400	Weak transcription	Spleen	Spleen
5	chr19:42681800-42703600	Weak transcription	Right Atrium	heart
6	chr19:42682400-42684400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:42682400-42684400	Bivalent Enhancer	Fetal Brain Male	brain
8	chr19:42683000-42684400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:42683200-42683800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:42683200-42683800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr19:42683200-42684200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:42683400-42683800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:42683400-42683800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:42683400-42684000	Bivalent Enhancer	Primary T cells from cord blood	blood
15	chr19:42683400-42684200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:42683400-42684200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:42683400-42684600	Bivalent Enhancer	Fetal Brain Female	brain
18	chr19:42683600-42683800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
19	chr19:42683600-42683800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:42683600-42683800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:42683600-42683800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
22	chr19:42683600-42683800	Bivalent Enhancer	Dnd41	blood
23	chr19:42683600-42684000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr19:42683600-42684000	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr19:42683600-42684200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr19:42683600-42684800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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