Variant report

Variant	rs11667718
Chromosome Location	chr19:57079202-57079203
allele	C/T
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	MXI1	chr19:57078013-57079833	IMR90	lung:	n/a	chr19:57078881-57078896
2	SP1	chr19:57078383-57079215	A549	lung:	n/a	chr19:57078942-57078951 chr19:57078828-57078838 chr19:57078390-57078402 chr19:57078390-57078402 chr19:57078828-57078838 chr19:57078391-57078400
3	MAZ	chr19:57078097-57079602	IMR90	lung:	n/a	n/a
4	POLR2A	chr19:57078223-57079261	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:57078289-57079234	GM18951	blood:	n/a	n/a
6	POLR2A	chr19:57078371-57079344	GM12892	blood:	n/a	n/a
7	GABPA	chr19:57078561-57079309	A549	lung:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
8	TCF12	chr19:57078375-57079474	A549	lung:	n/a	n/a
9	CREB1	chr19:57078643-57079207	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:57078671-57079232	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:57078887-57079305	GM12878	blood:	n/a	n/a
12	GABPA	chr19:57078438-57079256	HL-60	blood:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
13	FOXP2	chr19:57078720-57079240	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr19:57078336-57079301	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr19:57078404-57079213	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:57078505-57079236	SK-N-SH	brain:	n/a	n/a
17	TAF1	chr19:57078299-57079270	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr19:57078247-57079358	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr19:57078389-57079219	HUVEC	blood vessel:	n/a	n/a
20	E2F6	chr19:57078550-57079539	A549	lung:	n/a	chr19:57078967-57078976 chr19:57079111-57079120
21	MAX	chr19:57078557-57079388	ECC-1	luminal epithelium:	n/a	n/a
22	SRF	chr19:57078608-57079240	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr19:57078705-57079372	H1-hESC	embryonic stem cell:	n/a	n/a
24	GATA3	chr19:57078475-57079444	A549	lung:	n/a	chr19:57079320-57079333 chr19:57079322-57079330 chr19:57079308-57079318
25	POLR2A	chr19:57078335-57079233	GM15510	blood:	n/a	n/a
26	POLR2A	chr19:57078434-57079381	GM18505	blood:	n/a	n/a
27	POLR2A	chr19:57078409-57079234	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:57078589-57079222	GM12878	blood:	n/a	n/a
29	YY1	chr19:57078362-57079267	GM12892	blood:	n/a	chr19:57078372-57078386 chr19:57078967-57078976
30	TBP	chr19:57078531-57079252	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr19:57078321-57079394	SK-N-SH_RA	brain:	n/a	chr19:57078372-57078386 chr19:57078967-57078976 chr19:57079284-57079298
32	SRF	chr19:57078701-57079254	ECC-1	luminal epithelium:	n/a	n/a
33	TEAD4	chr19:57078930-57079216	H1-hESC	embryonic stem cell:	n/a	n/a
34	YY1	chr19:57078367-57079250	ECC-1	luminal epithelium:	n/a	chr19:57078372-57078386 chr19:57078967-57078976
35	SP1	chr19:57078442-57079256	A549	lung:	n/a	chr19:57078942-57078951 chr19:57078828-57078838 chr19:57078828-57078838
36	YY1	chr19:57078361-57079231	SK-N-SH_RA	brain:	n/a	chr19:57078372-57078386 chr19:57078967-57078976
37	MAX	chr19:57078168-57079577	A549	lung:	n/a	n/a
38	E2F6	chr19:57078762-57079286	A549	lung:	n/a	chr19:57078967-57078976 chr19:57079111-57079120
39	POLR2A	chr19:57078579-57079273	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr19:57078680-57079237	HUVEC	blood vessel:	n/a	n/a
41	MAX	chr19:57078252-57079388	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr19:57078136-57079264	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr19:57078643-57079299	A549	lung:	n/a	n/a
44	SIN3A	chr19:57078384-57079501	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr19:57078743-57079652	H1-hESC	embryonic stem cell:	n/a	chr19:57078881-57078896
46	RFX5	chr19:57077911-57079575	SK-N-SH	brain:	n/a	n/a
47	ELF1	chr19:57078218-57079535	GM12878	blood:	n/a	chr19:57078836-57078847 chr19:57079127-57079136
48	TAF1	chr19:57078509-57079234	ECC-1	luminal epithelium:	n/a	n/a
49	ELF1	chr19:57078315-57079298	SK-N-SH	brain:	n/a	chr19:57078836-57078847 chr19:57079127-57079136
50	POLR2A	chr19:57078816-57079207	Gliobla	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF470-1	chr19:57079018-57079407	NONHSAT068176

Variant related genes	Relation type
ENSG00000269696	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1052284	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670421	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672842	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17239746	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869897	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35452527	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3752180	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399350	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801341	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67585376	0.94[ASN][1000 genomes]
rs7252017	0.88[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259531	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs874104	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57077400-57079400	Active TSS	Brain Anterior Caudate	brain
2	chr19:57077400-57079400	Active TSS	Brain Hippocampus Middle	brain
3	chr19:57077400-57080000	ZNF genes & repeats	GM12878-XiMat	blood
4	chr19:57077600-57079600	Active TSS	Aorta	Aorta
5	chr19:57077600-57079800	Active TSS	Rectal Smooth Muscle	rectum
6	chr19:57077600-57082600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:57077800-57079400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:57077800-57079400	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr19:57077800-57079400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:57077800-57079400	Active TSS	Right Atrium	heart
11	chr19:57077800-57079400	Active TSS	Osteobl	bone
12	chr19:57077800-57079800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:57077800-57079800	Active TSS	Psoas Muscle	Psoas
14	chr19:57077800-57080000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:57078000-57079400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:57078000-57079400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:57078000-57079400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:57078000-57079400	Active TSS	Muscle Satellite Cultured Cells	--
19	chr19:57078000-57079400	Active TSS	Brain Angular Gyrus	brain
20	chr19:57078000-57079400	Active TSS	Brain Substantia Nigra	brain
21	chr19:57078000-57079400	Active TSS	Ovary	ovary
22	chr19:57078000-57079400	Active TSS	Right Ventricle	heart
23	chr19:57078000-57079600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:57078000-57079600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr19:57078000-57079800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr19:57078000-57079800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:57078000-57079800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:57078000-57079800	Active TSS	Fetal Kidney	kidney
29	chr19:57078000-57079800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:57078000-57080000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr19:57078000-57080000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:57078000-57080000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:57078000-57080000	Active TSS	HSMMtube	muscle
34	chr19:57078000-57080000	Active TSS	NHLF	lung
35	chr19:57078200-57079400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:57078200-57079400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:57078200-57079400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:57078200-57079400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:57078200-57079400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:57078200-57079400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:57078200-57079400	Active TSS	Colon Smooth Muscle	Colon
42	chr19:57078200-57079400	Active TSS	Fetal Heart	heart
43	chr19:57078200-57079400	Active TSS	Fetal Intestine Large	intestine
44	chr19:57078200-57079400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:57078200-57079600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:57078200-57079600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:57078200-57079600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:57078200-57079800	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:57078200-57079800	ZNF genes & repeats	Esophagus	oesophagus
50	chr19:57078200-57080200	Active TSS	NHDF-Ad	bronchial

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