Variant report

Variant	rs193040
Chromosome Location	chr19:53073605-53073606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:303)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:303 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:53073323-53074091	GM12892	blood:	n/a	n/a
2	HMGN3	chr19:53073359-53074188	K562	blood:	n/a	n/a
3	NR2F2	chr19:53073268-53073972	K562	blood:	n/a	n/a
4	SP1	chr19:53073128-53073756	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF1	chr19:53073391-53073647	Hela-S3	cervix:	n/a	n/a
6	GABPA	chr19:53073303-53074051	SK-N-SH	brain:	n/a	n/a
7	EBF1	chr19:53073445-53073980	GM12878	blood:	n/a	chr19:53073714-53073724 chr19:53073715-53073724 chr19:53073713-53073724 chr19:53073713-53073726
8	MAX	chr19:53073468-53074078	GM12878	blood:	n/a	chr19:53074033-53074043
9	ZBTB33	chr19:53073383-53074121	SK-N-SH	brain:	n/a	n/a
10	MYC	chr19:53073597-53073902	H1-hESC	embryonic stem cell:	n/a	n/a
11	GTF2F1	chr19:53073498-53073905	K562	blood:	n/a	n/a
12	SPI1	chr19:53073419-53073936	GM12878	blood:	n/a	chr19:53073722-53073735
13	POLR2A	chr19:53073002-53075041	GM12878	blood:	n/a	n/a
14	MAX	chr19:53073307-53073686	K562	blood:	n/a	n/a
15	TBL1XR1	chr19:53073356-53073883	K562	blood:	n/a	n/a
16	POLR2A	chr19:53073334-53074104	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:53073314-53074135	K562	blood:	n/a	n/a
18	HCFC1	chr19:53073212-53074110	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr19:53073480-53073630	GM12872	blood:	n/a	n/a
20	TAF1	chr19:53073461-53073794	K562	blood:	n/a	n/a
21	SRF	chr19:53073280-53074193	MCF-7	breast:	n/a	n/a
22	POLR2A	chr19:53073292-53074165	GM12878	blood:	n/a	n/a
23	TAF1	chr19:53073398-53073712	GM12878	blood:	n/a	n/a
24	REST	chr19:53073451-53073672	PFSK-1	brain:	n/a	n/a
25	PML	chr19:53073471-53073718	GM12878	blood:	n/a	n/a
26	RELA	chr19:53073280-53074090	GM15510	blood:	n/a	n/a
27	USF1	chr19:53073408-53073625	SK-N-SH_RA	brain:	n/a	n/a
28	RFX5	chr19:53073452-53073890	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:53073406-53074301	GM12891	blood:	n/a	n/a
30	TAF1	chr19:53073418-53073787	GM12878	blood:	n/a	n/a
31	CTCF	chr19:53073360-53073610	GM12875	blood:	n/a	n/a
32	GABPA	chr19:53073236-53074051	MCF-7	breast:	n/a	n/a
33	FOSL2	chr19:53072997-53073704	HepG2	liver:	n/a	n/a
34	MAX	chr19:53073376-53074051	K562	blood:	n/a	chr19:53074033-53074043
35	ZNF143	chr19:53073502-53074019	K562	blood:	n/a	n/a
36	SPI1	chr19:53073593-53073903	HL-60	blood:	n/a	chr19:53073722-53073735
37	POLR2A	chr19:53073246-53074018	GM12878	blood:	n/a	n/a
38	MXI1	chr19:53072742-53074375	SK-N-SH	brain:	n/a	chr19:53073030-53073039
39	CHD2	chr19:53073339-53074084	GM12878	blood:	n/a	chr19:53074031-53074041
40	POLR2A	chr19:53073372-53074034	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr19:53073381-53074120	K562	blood:	n/a	n/a
42	POLR2A	chr19:53072882-53074076	H1-hESC	embryonic stem cell:	n/a	n/a
43	NRF1	chr19:53073320-53074036	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:53073011-53073962	HepG2	liver:	n/a	n/a
45	CTCF	chr19:53073460-53073610	AG09319	gingival:	n/a	n/a
46	TAF1	chr19:53073390-53073799	GM12891	blood:	n/a	n/a
47	ZBTB33	chr19:53073398-53074158	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr19:53072963-53074749	GM12892	blood:	n/a	n/a
49	CBX3	chr19:53073512-53073861	K562	blood:	n/a	n/a
50	POLR2A	chr19:53073007-53074057	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:53073577-53073627	PrEC	prostate:	n/a
2	chr19:53073577-53073627	T-47D	breast:	n/a
3	chr19:53073577-53073627	NHBE	bronchial:	n/a
4	chr19:53073577-53073627	SK-N-MC	brain:	n/a
5	chr19:53073577-53073627	HUVEC	blood vessel:	n/a
6	chr19:53073577-53073627	GM12891	blood:	n/a
7	chr19:53073577-53073627	GM06990	blood:	n/a
8	chr19:53073577-53073627	Hela-S3	cervix:	n/a
9	chr19:53073577-53073627	HepG2	liver:	n/a
10	chr19:53073577-53073627	HCM	heart:	n/a
11	chr19:53073577-53073627	U87	brain:	n/a
12	chr19:53073577-53073627	ECC-1	luminal epithelium:	n/a
13	chr19:53073577-53073627	SAEC	small airway:	n/a
14	chr19:53073577-53073627	ProgFib	skin:	n/a
15	chr19:53073577-53073627	HEEpiC	esophagus:	n/a
16	chr19:53073577-53073627	K562	blood:	n/a
17	chr19:53073577-53073627	MCF-7	breast:	n/a
18	chr19:53073577-53073627	ovcar-3	ovarian:	n/a
19	chr19:53073577-53073627	HAEpiC	amniotic membrane:	n/a
20	chr19:53073577-53073627	BJ	skin:	n/a
21	chr19:53073577-53073627	HRCEpiC	kidney:	n/a
22	chr19:53073577-53073627	PFSK-1	brain:	n/a
23	chr19:53073577-53073627	HCPEpiC	choroid plexus:	n/a
24	chr19:53073577-53073627	A549	lung:	n/a
25	chr19:53073577-53073627	GM19239	blood:	n/a
26	chr19:53073577-53073627	Jurkat	blood:	n/a
27	chr19:53073577-53073627	SKMC	muscle:	n/a
28	chr19:53073577-53073627	NB4	blood:	n/a
29	chr19:53073577-53073627	PANC-1	pancreas:	n/a
30	chr19:53073577-53073627	HRE	kidney:	n/a
31	chr19:53073577-53073627	AG04450	lung:	fetal
32	chr19:53073577-53073627	IMR90	lung:	fetal
33	chr19:53073577-53073627	AG09309	skin:	n/a
34	chr19:53073577-53073627	HCF	heart:	n/a
35	chr19:53073577-53073627	SK-N-SH	brain:	n/a
36	chr19:53073577-53073627	HCT-116	colon:	n/a
37	chr19:53073577-53073627	MCF10A-Er-Src	breast:	n/a
38	chr19:53073577-53073627	GM12892	blood:	n/a
39	chr19:53073577-53073627	Hepatocyte	liver:	n/a
40	chr19:53073577-53073627	HMEC	breast:	n/a
41	chr19:53073577-53073627	HPAEpiC	pulmonary alveolar:	n/a
42	chr19:53073577-53073627	H1-hESC	embryonic stem cell:	embryo
43	chr19:53073577-53073627	HRPEpiC	eye:	n/a
44	chr19:53073577-53073627	AG09319	gingival:	n/a
45	chr19:53073577-53073627	BE2_C	brain:	n/a
46	chr19:53073577-53073627	CMK	blood:	n/a
47	chr19:53073577-53073627	HEK293	kidney:	embryo
48	chr19:53073577-53073627	Caco-2	colon:	n/a
49	chr19:53073577-53073627	NT2-D1	testis:	n/a
50	chr19:53073577-53073627	AG10803	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:53073504..53075016-chr19:53086712..53089202,2	MCF-7	breast:
2	chr19:53073369..53074894-chr19:53098457..53100751,2	MCF-7	breast:
3	chr19:53029127..53032188-chr19:53072538..53075129,3	K562	blood:
4	chr19:53029450..53032188-chr19:53072538..53074123,2	K562	blood:

No data

Variant related genes	Relation type
ZNF701	TF binding region
ZNF701	CpG island
ENSG00000123870	Chromatin interaction
ENSG00000198482	Chromatin interaction
ENSG00000268886	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs329945	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs329966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329967	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53062000-53077800	ZNF genes & repeats	Liver	Liver
2	chr19:53072400-53074000	Active TSS	Osteobl	bone
3	chr19:53072400-53074200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr19:53072600-53074000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr19:53072600-53074000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:53072600-53074000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:53072600-53074400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:53072600-53074600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:53072600-53074600	Active TSS	Fetal Brain Female	brain
10	chr19:53072800-53073800	Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr19:53072800-53073800	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr19:53072800-53073800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:53072800-53073800	Active TSS	Duodenum Mucosa	Duodenum
14	chr19:53072800-53073800	Active TSS	Fetal Lung	lung
15	chr19:53072800-53073800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:53072800-53073800	Active TSS	Right Ventricle	heart
17	chr19:53072800-53073800	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr19:53072800-53073800	Active TSS	NH-A	brain
19	chr19:53072800-53074000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:53072800-53074000	Active TSS	Muscle Satellite Cultured Cells	--
21	chr19:53072800-53074000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:53072800-53074000	Active TSS	Brain Angular Gyrus	brain
23	chr19:53072800-53074000	Active TSS	Brain Hippocampus Middle	brain
24	chr19:53072800-53074000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr19:53072800-53074000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:53072800-53074000	Active TSS	Colon Smooth Muscle	Colon
27	chr19:53072800-53074000	Active TSS	Fetal Brain Male	brain
28	chr19:53072800-53074000	Active TSS	Placenta Amnion	Placenta Amnion
29	chr19:53072800-53074000	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:53072800-53074000	Active TSS	Right Atrium	heart
31	chr19:53072800-53074000	Active TSS	HSMM	muscle
32	chr19:53072800-53074200	Active TSS	Left Ventricle	heart
33	chr19:53072800-53074400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:53072800-53074400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:53072800-53074400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:53072800-53074400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:53072800-53074400	Active TSS	Brain Anterior Caudate	brain
38	chr19:53072800-53074400	Active TSS	Brain Germinal Matrix	brain
39	chr19:53072800-53074400	Active TSS	Fetal Intestine Large	intestine
40	chr19:53072800-53074400	Active TSS	Fetal Kidney	kidney
41	chr19:53072800-53074400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:53072800-53074400	Active TSS	Fetal Stomach	stomach
43	chr19:53072800-53074400	Active TSS	Stomach Smooth Muscle	stomach
44	chr19:53072800-53074400	Active TSS	HSMMtube	muscle
45	chr19:53072800-53074600	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:53072800-53074600	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:53072800-53074600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:53072800-53074600	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:53072800-53074600	Active TSS	HepG2	liver
50	chr19:53072800-53074600	Active TSS	NHLF	lung

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