Variant report

Variant	rs892034
Chromosome Location	chr19:39368998-39368999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr19:39368787-39369052	GM12892	blood:	n/a	n/a
2	MYC	chr19:39368878-39369102	K562	blood:	n/a	chr19:39368925-39368935
3	POLR2A	chr19:39368504-39369160	GM12878	blood:	n/a	n/a
4	TAF1	chr19:39368675-39369150	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39368553-39369129	HCT-116	colon:	n/a	n/a
6	POLR2A	chr19:39368442-39369541	GM12892	blood:	n/a	n/a
7	MAX	chr19:39368633-39369133	GM12878	blood:	n/a	chr19:39368925-39368935
8	POU2F2	chr19:39368589-39369174	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:39368524-39369489	HepG2	liver:	n/a	n/a
10	HDAC2	chr19:39368794-39369163	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:39368650-39369082	HepG2	liver:	n/a	n/a
12	TBP	chr19:39368771-39369109	GM12878	blood:	n/a	n/a
13	POU2F2	chr19:39368799-39369076	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:39368618-39369184	HUVEC	blood vessel:	n/a	n/a
15	CHD2	chr19:39368697-39369183	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39368571-39369544	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:39368615-39369226	GM15510	blood:	n/a	n/a
18	EP300	chr19:39368810-39369245	GM12878	blood:	n/a	chr19:39368898-39368907
19	MAZ	chr19:39368718-39369089	K562	blood:	n/a	chr19:39368925-39368935
20	POLR2A	chr19:39368463-39369148	HCT-116	colon:	n/a	n/a
21	MTA3	chr19:39368293-39369480	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39368636-39369148	GM12891	blood:	n/a	n/a
23	MAZ	chr19:39368569-39369382	GM12878	blood:	n/a	chr19:39368925-39368935
24	MAX	chr19:39368707-39369107	NB4	blood:	n/a	chr19:39368925-39368935
25	POLR2A	chr19:39368570-39369191	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:39368472-39369229	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr19:39368758-39369047	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:39368515-39369373	GM18505	blood:	n/a	n/a
29	POLR2A	chr19:39368651-39369010	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr19:39368632-39369143	K562	blood:	n/a	n/a
31	RUNX3	chr19:39368653-39369126	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:39368596-39369168	GM12892	blood:	n/a	n/a
33	HEY1	chr19:39368636-39369218	HepG2	liver:	n/a	n/a
34	GABPA	chr19:39368633-39369094	K562	blood:	n/a	n/a
35	POLR2A	chr19:39368628-39369190	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:39368774-39369116	K562	blood:	n/a	n/a
37	POLR2A	chr19:39368684-39369193	NB4	blood:	n/a	n/a
38	GABPA	chr19:39368645-39369027	HepG2	liver:	n/a	n/a
39	ELF1	chr19:39368597-39369096	K562	blood:	n/a	n/a
40	POLR2A	chr19:39368583-39369189	GM12891	blood:	n/a	n/a
41	MTA3	chr19:39368639-39369075	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:39368600-39369098	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:39368689-39369207	GM10847	blood:	n/a	n/a
44	ETS1	chr19:39368678-39369068	GM12878	blood:	n/a	chr19:39368900-39368911 chr19:39368899-39368910
45	POLR2A	chr19:39368470-39369256	HL-60	blood:	n/a	n/a
46	POLR2A	chr19:39368497-39369155	HUVEC	blood vessel:	n/a	n/a
47	HCFC1	chr19:39368846-39369046	K562	blood:	n/a	n/a
48	SMC3	chr19:39368864-39369110	GM12878	blood:	n/a	n/a
49	YY1	chr19:39368677-39369004	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:39368553-39369205	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39358481..39361924-chr19:39367868..39369637,3	K562	blood:
2	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
3	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
4	chr19:39360424..39362257-chr19:39368137..39371034,2	K562	blood:
5	chr19:39339112..39343595-chr19:39368855..39373078,6	MCF-7	breast:

No data

Variant related genes	Relation type
RINL	TF binding region
ENSG00000269050	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10424892	0.93[GIH][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083482	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1529713	0.93[GIH][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6508823	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8108906	0.89[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]

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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs892034	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39360800-39371400	Weak transcription	NHLF	lung
2	chr19:39360800-39379200	Weak transcription	NHDF-Ad	bronchial
3	chr19:39361000-39370000	Weak transcription	Aorta	Aorta
4	chr19:39361000-39379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:39361000-39380200	Weak transcription	Psoas Muscle	Psoas
6	chr19:39361200-39369200	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:39361200-39369400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:39361200-39369400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:39361200-39369600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:39361200-39369800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:39361200-39369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:39361200-39369800	Weak transcription	Pancreas	Pancrea
13	chr19:39361200-39370000	Weak transcription	Brain Substantia Nigra	brain
14	chr19:39361200-39370400	Weak transcription	Brain Angular Gyrus	brain
15	chr19:39361200-39370600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:39361200-39370800	Weak transcription	Ovary	ovary
17	chr19:39361200-39371000	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:39361200-39371200	Weak transcription	Liver	Liver
19	chr19:39361200-39376800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:39361400-39369200	Weak transcription	Brain Germinal Matrix	brain
21	chr19:39361400-39369200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:39361600-39369200	Weak transcription	Right Ventricle	heart
23	chr19:39361600-39369800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:39362400-39369000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:39363800-39369600	Weak transcription	Fetal Brain Female	brain
26	chr19:39364600-39369200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:39365400-39379400	Weak transcription	Osteobl	bone
28	chr19:39366400-39370600	Enhancers	HSMMtube	muscle
29	chr19:39366800-39369800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:39367200-39369000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr19:39367400-39369800	Weak transcription	HSMM	muscle
32	chr19:39367400-39371400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39367800-39369600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr19:39367800-39369800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39368000-39369000	Active TSS	GM12878-XiMat	blood
36	chr19:39368000-39369200	Enhancers	Fetal Lung	lung
37	chr19:39368000-39374200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:39368200-39369000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:39368200-39369400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr19:39368200-39369400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr19:39368200-39369600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr19:39368200-39369600	Enhancers	Adipose Nuclei	Adipose
43	chr19:39368200-39369600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr19:39368200-39369600	Enhancers	HUVEC	blood vessel
45	chr19:39368200-39369800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr19:39368200-39370000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr19:39368200-39370200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr19:39368200-39370400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr19:39368200-39370400	Enhancers	Small Intestine	intestine
50	chr19:39368400-39369000	Active TSS	Primary T cells from cord blood	blood

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