Variant report

Variant	rs4801341
Chromosome Location	chr19:57078645-57078646
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	POLR2A	chr19:57078623-57078858	GM12891	blood:	n/a	n/a
2	MXI1	chr19:57078013-57079833	IMR90	lung:	n/a	chr19:57078881-57078896
3	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
4	MAZ	chr19:57078097-57079602	IMR90	lung:	n/a	n/a
5	POLR2A	chr19:57078223-57079261	SK-N-MC	brain:	n/a	n/a
6	MTA3	chr19:57078420-57078753	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:57078289-57079234	GM18951	blood:	n/a	n/a
8	POLR2A	chr19:57078371-57079344	GM12892	blood:	n/a	n/a
9	SIN3AK20	chr19:57078575-57078989	H1-hESC	embryonic stem cell:	n/a	n/a
10	GABPA	chr19:57078561-57079309	A549	lung:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
11	TCF12	chr19:57078375-57079474	A549	lung:	n/a	n/a
12	CREB1	chr19:57078643-57079207	H1-hESC	embryonic stem cell:	n/a	n/a
13	ELF1	chr19:57078590-57078912	K562	blood:	n/a	chr19:57078836-57078847
14	GTF2F1	chr19:57078463-57078784	H1-hESC	embryonic stem cell:	n/a	n/a
15	GABPA	chr19:57078438-57079256	HL-60	blood:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
16	SIX5	chr19:57078633-57078925	H1-hESC	embryonic stem cell:	n/a	chr19:57078799-57078808 chr19:57078797-57078806
17	SIX5	chr19:57078402-57079096	A549	lung:	n/a	chr19:57078799-57078808 chr19:57078797-57078806
18	POLR2A	chr19:57078336-57079301	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr19:57078404-57079213	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:57078505-57079236	SK-N-SH	brain:	n/a	n/a
21	TAF1	chr19:57078299-57079270	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr19:57078247-57079358	H1-neurons	neurons:	n/a	n/a
23	SIN3AK20	chr19:57078643-57078891	H1-hESC	embryonic stem cell:	n/a	n/a
24	GABPA	chr19:57078534-57079179	SK-N-SH	brain:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
25	POLR2A	chr19:57078389-57079219	HUVEC	blood vessel:	n/a	n/a
26	E2F6	chr19:57078550-57079539	A549	lung:	n/a	chr19:57078967-57078976 chr19:57079111-57079120
27	ELK1	chr19:57078611-57078995	GM12878	blood:	n/a	chr19:57078836-57078845 chr19:57078836-57078845
28	MAX	chr19:57078557-57079388	ECC-1	luminal epithelium:	n/a	n/a
29	SRF	chr19:57078608-57079240	ECC-1	luminal epithelium:	n/a	n/a
30	ETS1	chr19:57078608-57079004	A549	lung:	n/a	chr19:57078836-57078845 chr19:57078795-57078808 chr19:57078836-57078845 chr19:57078796-57078809 chr19:57078834-57078844 chr19:57078833-57078849
31	RUNX3	chr19:57078638-57079169	GM12878	blood:	n/a	n/a
32	GATA3	chr19:57078475-57079444	A549	lung:	n/a	chr19:57079320-57079333 chr19:57079322-57079330 chr19:57079308-57079318
33	POLR2A	chr19:57078335-57079233	GM15510	blood:	n/a	n/a
34	POLR2A	chr19:57078434-57079381	GM18505	blood:	n/a	n/a
35	SIX5	chr19:57078635-57079086	H1-hESC	embryonic stem cell:	n/a	chr19:57078799-57078808 chr19:57078797-57078806
36	POLR2A	chr19:57078409-57079234	GM12892	blood:	n/a	n/a
37	GABPA	chr19:57078625-57079201	GM12878	blood:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
38	MXI1	chr19:57078634-57079098	GM12878	blood:	n/a	chr19:57078881-57078896
39	POLR2A	chr19:57078589-57079222	GM12878	blood:	n/a	n/a
40	YY1	chr19:57078362-57079267	GM12892	blood:	n/a	chr19:57078372-57078386 chr19:57078967-57078976
41	TBP	chr19:57078531-57079252	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr19:57078321-57079394	SK-N-SH_RA	brain:	n/a	chr19:57078372-57078386 chr19:57078967-57078976 chr19:57079284-57079298
43	POLR2A	chr19:57078625-57078979	HUVEC	blood vessel:	n/a	n/a
44	GABPA	chr19:57078572-57079033	H1-hESC	embryonic stem cell:	n/a	n/a
45	YY1	chr19:57078374-57079073	GM12878	blood:	n/a	chr19:57078967-57078976
46	ETS1	chr19:57078344-57079124	A549	lung:	n/a	chr19:57078836-57078845 chr19:57078795-57078808 chr19:57078836-57078845 chr19:57078796-57078809 chr19:57078834-57078844 chr19:57078374-57078385 chr19:57078833-57078849
47	GABPA	chr19:57078511-57079152	HL-60	blood:	n/a	chr19:57079055-57079064 chr19:57079057-57079066 chr19:57079110-57079121 chr19:57079107-57079121
48	YY1	chr19:57078367-57079250	ECC-1	luminal epithelium:	n/a	chr19:57078372-57078386 chr19:57078967-57078976
49	ELF1	chr19:57078425-57079062	A549	lung:	n/a	chr19:57078836-57078847
50	SP1	chr19:57078519-57079068	H1-hESC	embryonic stem cell:	n/a	chr19:57078942-57078951 chr19:57078828-57078838 chr19:57078828-57078838

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF667-2	chr19:57078442-57078774	ENSG00000245443
2	lnc-ZNF667-2	chr19:57078442-57078833	NONHSAT068173
3	lnc-ZNF667-2	chr19:57078442-57078780	ENSG00000269696.1

Variant related genes	Relation type
ZNF470	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1052284	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667718	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]
rs11670421	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672842	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17239746	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2869897	1.00[ASN][1000 genomes]
rs35452527	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752180	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[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];0.99[ASN][1000 genomes]
rs399350	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67585376	0.94[ASN][1000 genomes]
rs7259531	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs874104	0.83[AFR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4801341	ZNF606	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57077400-57079000	Active TSS	Primary T cells from cord blood	blood
2	chr19:57077400-57079200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:57077400-57079400	Active TSS	Brain Anterior Caudate	brain
4	chr19:57077400-57079400	Active TSS	Brain Hippocampus Middle	brain
5	chr19:57077400-57080000	ZNF genes & repeats	GM12878-XiMat	blood
6	chr19:57077600-57079200	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr19:57077600-57079600	Active TSS	Aorta	Aorta
8	chr19:57077600-57079800	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:57077600-57082600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:57077800-57079200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:57077800-57079200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:57077800-57079200	Active TSS	Left Ventricle	heart
13	chr19:57077800-57079200	Active TSS	Stomach Mucosa	stomach
14	chr19:57077800-57079200	Active TSS	Stomach Smooth Muscle	stomach
15	chr19:57077800-57079400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:57077800-57079400	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr19:57077800-57079400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:57077800-57079400	Active TSS	Right Atrium	heart
19	chr19:57077800-57079400	Active TSS	Osteobl	bone
20	chr19:57077800-57079800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:57077800-57079800	Active TSS	Psoas Muscle	Psoas
22	chr19:57077800-57080000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr19:57078000-57078800	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:57078000-57079000	Active TSS	Fetal Brain Male	brain
25	chr19:57078000-57079200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:57078000-57079200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr19:57078000-57079200	Active TSS	Duodenum Mucosa	Duodenum
28	chr19:57078000-57079200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr19:57078000-57079200	Active TSS	Fetal Brain Female	brain
30	chr19:57078000-57079200	Active TSS	Fetal Lung	lung
31	chr19:57078000-57079200	Active TSS	Fetal Muscle Leg	muscle
32	chr19:57078000-57079200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr19:57078000-57079200	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr19:57078000-57079200	Active TSS	Thymus	Thymus
35	chr19:57078000-57079200	Active TSS	HMEC	breast
36	chr19:57078000-57079200	Active TSS	HSMM	muscle
37	chr19:57078000-57079200	Active TSS	NH-A	brain
38	chr19:57078000-57079400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:57078000-57079400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:57078000-57079400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:57078000-57079400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:57078000-57079400	Active TSS	Brain Angular Gyrus	brain
43	chr19:57078000-57079400	Active TSS	Brain Substantia Nigra	brain
44	chr19:57078000-57079400	Active TSS	Ovary	ovary
45	chr19:57078000-57079400	Active TSS	Right Ventricle	heart
46	chr19:57078000-57079600	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:57078000-57079600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr19:57078000-57079800	Active TSS	H1 Cell Line	embryonic stem cell
49	chr19:57078000-57079800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:57078000-57079800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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