Variant report

Variant	rs167769
Chromosome Location	chr12:57503775-57503776
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	chr12:57503549-57506510	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:57503263-57506255	GM12878	blood:	n/a	n/a
3	WRNIP1	chr12:57503667-57504745	GM12878	blood:	n/a	n/a
4	CTCF	chr12:57503770-57506732	A549	lung:	n/a	chr12:57506277-57506287 chr12:57506274-57506292 chr12:57506276-57506289 chr12:57505530-57505543 chr12:57506280-57506289 chr12:57506269-57506290
5	POLR2A	chr12:57503679-57506503	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:57503440-57506280	GM12878	blood:	n/a	n/a
7	NFIC	chr12:57503616-57503959	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:57503715-57506448	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:57503624-57506409	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:57503454-57506445	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:57503719-57506533	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:57503682-57503782	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:57503597-57506381	GM12892	blood:	n/a	n/a
14	JUN	chr12:57503568-57506684	K562	blood:	n/a	chr12:57506060-57506070 chr12:57506062-57506069 chr12:57506061-57506069 chr12:57506060-57506070 chr12:57506060-57506070 chr12:57506060-57506070 chr12:57506061-57506069
15	POLR2A	chr12:57503459-57506401	K562	blood:	n/a	n/a
16	STAT5A	chr12:57503622-57506486	GM12878	blood:	n/a	chr12:57505650-57505662 chr12:57503642-57503654 chr12:57504117-57504129 chr12:57504633-57504645 chr12:57504673-57504685 chr12:57504334-57504346
17	POLR2A	chr12:57503439-57506359	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:57503224-57506154	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:57503455-57506535	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:57503383-57506027	GM12892	blood:	n/a	n/a
21	TAF1	chr12:57503766-57504400	H1-hESC	embryonic stem cell:	n/a	n/a
22	MTA3	chr12:57503437-57506543	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:57503635-57506439	K562	blood:	n/a	n/a
24	POLR2A	chr12:57503451-57506183	GM12892	blood:	n/a	n/a
25	POLR2A	chr12:57503679-57504325	GM12891	blood:	n/a	n/a
26	POLR2A	chr12:57503750-57506402	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57145013..57147462-chr12:57502866..57505810,2	K562	blood:
2	chr12:57399687..57402362-chr12:57503183..57504772,2	K562	blood:
3	chr12:57503657..57505571-chr12:57633144..57635959,2	MCF-7	breast:

Variant related genes	Relation type
STAT6	TF binding region
ENSG00000166860	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000198056	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11172106	0.82[CEU][hapmap]
rs12368672	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs3001425	0.93[EUR][1000 genomes]
rs3001427	0.94[EUR][1000 genomes]
rs3122929	0.94[EUR][1000 genomes]
rs324011	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324012	0.81[ASN][1000 genomes]
rs324020	1.00[JPT][hapmap]
rs703816	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs703817	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs841718	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Eosinophilic esophagitis (pediatric)	20208534	GWAS catalog
Eosinophilic esophagitis	25407941	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs167769	KRT2	cis	parietal	SCAN
rs167769	ESPL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57486600-57503800	Weak transcription	Brain Substantia Nigra	brain
2	chr12:57490000-57503800	Weak transcription	NH-A	brain
3	chr12:57490000-57504000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:57494000-57504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:57496800-57504000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:57498400-57503800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:57502400-57503800	Weak transcription	Fetal Heart	heart
8	chr12:57502400-57503800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:57502800-57505400	Active TSS	GM12878-XiMat	blood
10	chr12:57502800-57506400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:57503000-57504000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr12:57503000-57504200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:57503000-57504200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:57503000-57505800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:57503200-57503800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:57503200-57503800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
17	chr12:57503200-57503800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr12:57503200-57503800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr12:57503200-57503800	Enhancers	Brain Anterior Caudate	brain
20	chr12:57503200-57503800	Enhancers	Brain Hippocampus Middle	brain
21	chr12:57503200-57503800	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr12:57503200-57503800	Enhancers	Gastric	stomach
23	chr12:57503200-57503800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr12:57503200-57503800	Transcr. at gene 5' and 3'	NHEK	skin
25	chr12:57503200-57504000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr12:57503200-57504000	Flanking Active TSS	Fetal Stomach	stomach
27	chr12:57503200-57504000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr12:57503200-57504000	Flanking Active TSS	A549	lung
29	chr12:57503200-57504200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr12:57503200-57504200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:57503200-57504200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:57503200-57504200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr12:57503200-57504200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr12:57503200-57504200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr12:57503200-57504200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:57503200-57504200	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr12:57503200-57504200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:57503200-57504200	Flanking Active TSS	Hela-S3	cervix
39	chr12:57503200-57504400	Flanking Active TSS	HMEC	breast
40	chr12:57503200-57504400	Flanking Active TSS	Osteobl	bone
41	chr12:57503200-57504800	Flanking Active TSS	Fetal Thymus	thymus
42	chr12:57503200-57505200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr12:57503200-57505400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:57503200-57505800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:57503200-57505800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:57503200-57506000	Active TSS	Ovary	ovary
47	chr12:57503200-57506200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr12:57503200-57506400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:57503200-57506600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:57503400-57503800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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