Variant report

Variant	rs329936
Chromosome Location	chr19:53088568-53088569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:53088425-53088741	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:53088425-53088791	K562	blood:	n/a	n/a
3	POLR2A	chr19:53088199-53088772	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:53088551-53088601	SAEC	small airway:	n/a
2	chr19:53088551-53088601	RPTEC	kidney:	n/a
3	chr19:53088551-53088601	Hela-S3	cervix:	n/a
4	chr19:53088551-53088601	GM12878	blood:	n/a
5	chr19:53088551-53088601	SKMC	muscle:	n/a
6	chr19:53088551-53088601	HRCEpiC	kidney:	n/a
7	chr19:53088551-53088601	AoSMC	blood vessel:	n/a
8	chr19:53088551-53088601	BE2_C	brain:	n/a
9	chr19:53088551-53088601	AG09319	gingival:	n/a
10	chr19:53088551-53088601	K562	blood:	n/a
11	chr19:53088551-53088601	HCT-116	colon:	n/a
12	chr19:53088551-53088601	U87	brain:	n/a
13	chr19:53088551-53088601	NHBE	bronchial:	n/a
14	chr19:53088551-53088601	HL-60	blood:	n/a
15	chr19:53088551-53088601	CMK	blood:	n/a
16	chr19:53088551-53088601	T-47D	breast:	n/a
17	chr19:53088551-53088601	HIPEpiC	eye:	n/a
18	chr19:53088551-53088601	PFSK-1	brain:	n/a
19	chr19:53088551-53088601	GM12892	blood:	n/a
20	chr19:53088551-53088601	Hepatocyte	liver:	n/a
21	chr19:53088551-53088601	BJ	skin:	n/a
22	chr19:53088551-53088601	GM19239	blood:	n/a
23	chr19:53088551-53088601	NHDF-neo	bronchial:	n/a
24	chr19:53088551-53088601	HepG2	liver:	n/a
25	chr19:53088551-53088601	ovcar-3	ovarian:	n/a
26	chr19:53088551-53088601	HCF	heart:	n/a
27	chr19:53088551-53088601	HCPEpiC	choroid plexus:	n/a
28	chr19:53088551-53088601	NH-A	brain:	n/a
29	chr19:53088551-53088601	IMR90	lung:	fetal
30	chr19:53088551-53088601	MCF-7	breast:	n/a
31	chr19:53088551-53088601	MCF10A-Er-Src	breast:	n/a
32	chr19:53088551-53088601	A549	lung:	n/a
33	chr19:53088551-53088601	H1-hESC	embryonic stem cell:	embryo
34	chr19:53088551-53088601	AG09309	skin:	n/a
35	chr19:53088551-53088601	GM06990	blood:	n/a
36	chr19:53088551-53088601	AG04450	lung:	fetal
37	chr19:53088551-53088601	HMEC	breast:	n/a
38	chr19:53088551-53088601	SK-N-SH	brain:	n/a
39	chr19:53088551-53088601	HUVEC	blood vessel:	n/a
40	chr19:53088551-53088601	PrEC	prostate:	n/a
41	chr19:53088551-53088601	HPAEpiC	pulmonary alveolar:	n/a
42	chr19:53088551-53088601	SK-N-SH_RA	brain:	n/a
43	chr19:53088551-53088601	NB4	blood:	n/a
44	chr19:53088551-53088601	HCM	heart:	n/a
45	chr19:53088551-53088601	HNPCEpiC	eye:	n/a
46	chr19:53088551-53088601	LNCaP	prostate:	n/a
47	chr19:53088551-53088601	NT2-D1	testis:	n/a
48	chr19:53088551-53088601	HEEpiC	esophagus:	n/a
49	chr19:53088551-53088601	SK-N-MC	brain:	n/a
50	chr19:53088551-53088601	ECC-1	luminal epithelium:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr19:53073504..53075016-chr19:53086712..53089202,2	MCF-7	breast:
2	chr19:53087080..53089827-chr19:53090383..53092275,2	K562	blood:
3	chr19:53086321..53088746-chr19:53090945..53093130,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-4	chr19:53088283-53088814	ENSG00000268886.1

No data

Variant related genes	Relation type
ZNF137P	TF binding region
ZNF137P	CpG island
ENSG00000123870	Chromatin interaction
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs364349	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427127	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433377	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436565	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454950	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564612	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73580214	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73580218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73580219	1.00[ASN][1000 genomes]
rs73580221	1.00[EUR][1000 genomes];1.00[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	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
3	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
4	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
5	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
6	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
7	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
8	esv3385321	chr19:53086990-53090388	ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
2	chr19:53075400-53089600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:53075400-53092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:53075400-53092400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:53075400-53092400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53076400-53096000	Strong transcription	Dnd41	blood
7	chr19:53079200-53092200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:53079400-53089400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:53079400-53090400	ZNF genes & repeats	Liver	Liver
10	chr19:53079400-53092200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr19:53079400-53094200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:53079400-53096000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:53079600-53089600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:53079600-53091800	ZNF genes & repeats	Thymus	Thymus
15	chr19:53079800-53089200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:53079800-53091000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:53080200-53089400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:53081600-53090200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:53082200-53089200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
20	chr19:53082800-53089200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
21	chr19:53083200-53091000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:53083400-53088800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr19:53083400-53089200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
24	chr19:53083400-53090400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:53083400-53091000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:53083600-53088600	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr19:53083600-53088600	ZNF genes & repeats	GM12878-XiMat	blood
28	chr19:53083600-53090400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:53083600-53090800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
30	chr19:53083600-53092400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:53083800-53088600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:53083800-53092400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:53084600-53091200	ZNF genes & repeats	Colonic Mucosa	Colon
34	chr19:53085400-53089200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:53085400-53089200	ZNF genes & repeats	NHEK	skin
36	chr19:53085400-53091200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:53085800-53088600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:53085800-53089200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:53086800-53090000	ZNF genes & repeats	Lung	lung
40	chr19:53087200-53088800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr19:53087200-53091000	ZNF genes & repeats	Spleen	Spleen
42	chr19:53087400-53088800	ZNF genes & repeats	Pancreas	Pancrea
43	chr19:53087400-53089000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:53087400-53091000	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr19:53087400-53091000	ZNF genes & repeats	Fetal Thymus	thymus
46	chr19:53087400-53095200	Weak transcription	Brain Anterior Caudate	brain
47	chr19:53087400-53103600	Weak transcription	Brain Substantia Nigra	brain
48	chr19:53087600-53089600	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr19:53087600-53089800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:53087600-53089800	Weak transcription	Brain Inferior Temporal Lobe	brain

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