Variant report

Variant	rs7260393
Chromosome Location	chr19:19886410-19886411
allele	C/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	HCFC1	chr19:19886407-19888705	Hela-S3	cervix:	n/a	n/a
2	SREBP1	chr19:19886186-19888557	GM12878	blood:	n/a	chr19:19887863-19887877
3	CUX1	chr19:19886307-19888068	K562	blood:	n/a	n/a
4	REST	chr19:19886302-19888021	H1-neurons	neurons:	n/a	chr19:19887772-19887780
5	MXI1	chr19:19886113-19889151	SK-N-SH	brain:	n/a	chr19:19886836-19886845

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19772600..19774395-chr19:19886060..19888388,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-1	chr19:19884687-19887232	ENSG00000266904.1

Variant related genes	Relation type
ENSG00000267419	TF binding region
ENSG00000105726	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11085277	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327770	0.99[ASN][1000 genomes]
rs16996320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808992	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72620573	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72620574	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72620575	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs737195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7260393	ZNF253	Cis_1M	lymphoblastoid	RTeQTL
rs7260393	ZNF506	cis	uninvolved skin	skin_eQTL
rs7260393	ZNF253	cis	Nerve Tibial	GTEx
rs7260393	ZNF506	cis	lesional skin	skin_eQTL
rs7260393	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs7260393	ZNF682	cis	Muscle Skeletal	GTEx
rs7260393	ZNF506	cis	normal skin	skin_eQTL
rs7260393	ZNF506	cis	Heart Left Ventricle	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19885200-19886600	Enhancers	Primary hematopoietic stem cells	blood
2	chr19:19885600-19886800	Enhancers	Spleen	Spleen
3	chr19:19885800-19886600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr19:19886000-19886600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:19886000-19888000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19886200-19886600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:19886200-19886600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr19:19886200-19886600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr19:19886200-19886600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:19886200-19886600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:19886200-19886600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:19886200-19886600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr19:19886200-19886600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr19:19886200-19886600	Flanking Active TSS	GM12878-XiMat	blood
15	chr19:19886200-19886800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:19886200-19886800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:19886200-19886800	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr19:19886200-19886800	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr19:19886200-19886800	Flanking Active TSS	K562	blood
20	chr19:19886200-19887000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:19886200-19887000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:19886200-19887000	Flanking Active TSS	Dnd41	blood
23	chr19:19886200-19887800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:19886200-19887800	Active TSS	Fetal Brain Male	brain
25	chr19:19886200-19888400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:19886200-19888400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:19886200-19888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr19:19886200-19888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19886200-19888600	Active TSS	A549	lung
30	chr19:19886400-19886600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:19886400-19886600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:19886400-19886600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:19886400-19886600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:19886400-19886600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:19886400-19886600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:19886400-19886600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr19:19886400-19886600	Enhancers	Primary B cells from cord blood	blood
38	chr19:19886400-19886600	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:19886400-19886600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:19886400-19886600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:19886400-19886600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr19:19886400-19886600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:19886400-19886600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr19:19886400-19886600	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr19:19886400-19886600	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr19:19886400-19886600	Enhancers	Colonic Mucosa	Colon
47	chr19:19886400-19886600	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr19:19886400-19886600	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr19:19886400-19886600	Flanking Active TSS	Fetal Kidney	kidney
50	chr19:19886400-19886600	Flanking Active TSS	Fetal Lung	lung

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