Variant report

Variant	rs35895760
Chromosome Location	chr19:52995824-52995825
allele	G/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	MAX	chr19:52995776-52996778	H1-hESC	embryonic stem cell:	n/a	chr19:52995948-52995958
2	TAF1	chr19:52995451-52996319	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr19:52995781-52996847	H1-hESC	embryonic stem cell:	n/a	chr19:52996018-52996026 chr19:52996383-52996395 chr19:52996425-52996437 chr19:52996019-52996026 chr19:52996018-52996026
4	CTCF	chr19:52995784-52996132	H1-hESC	embryonic stem cell:	n/a	chr19:52995951-52995964 chr19:52996074-52996084 chr19:52995949-52995967
5	E2F6	chr19:52995692-52996831	H1-hESC	embryonic stem cell:	n/a	chr19:52996018-52996026 chr19:52996383-52996395 chr19:52996425-52996437 chr19:52996019-52996026 chr19:52996018-52996026
6	ZNF143	chr19:52995823-52996209	H1-hESC	embryonic stem cell:	n/a	chr19:52996002-52996020
7	POLR2A	chr19:52995795-52996252	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr19:52995801-52996072	GM12878	blood:	n/a	chr19:52995947-52995959 chr19:52996005-52996014 chr19:52995948-52995957 chr19:52996037-52996046 chr19:52995948-52995962 chr19:52996036-52996048 chr19:52996038-52996047 chr19:52995949-52995958 chr19:52995948-52995958 chr19:52996036-52996048 chr19:52995937-52995946 chr19:52996006-52996015 chr19:52995936-52995948 chr19:52995936-52995948 chr19:52995947-52995959 chr19:52996005-52996014
9	POLR2A	chr19:52995747-52996306	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr19:52995696-52996253	H1-hESC	embryonic stem cell:	n/a	chr19:52995949-52995961
11	POLR2A	chr19:52995409-52996994	H1-hESC	embryonic stem cell:	n/a	n/a
12	POU2F2	chr19:52995430-52995826	GM12878	blood:	n/a	chr19:52995794-52995807
13	MAX	chr19:52995739-52996790	H1-hESC	embryonic stem cell:	n/a	chr19:52995948-52995958

Variant related genes	Relation type
ZNF578	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12461522	1.00[ASN][1000 genomes]
rs12462080	1.00[ASN][1000 genomes]
rs12971372	1.00[ASN][1000 genomes]
rs12977988	1.00[ASN][1000 genomes]
rs12985487	1.00[ASN][1000 genomes]
rs12986137	1.00[ASN][1000 genomes]
rs16983943	1.00[ASN][1000 genomes]
rs2061355	1.00[ASN][1000 genomes]
rs28570374	1.00[ASN][1000 genomes]
rs329948	1.00[ASN][1000 genomes]
rs329949	1.00[ASN][1000 genomes]
rs34106830	1.00[ASN][1000 genomes]
rs34203482	1.00[ASN][1000 genomes]
rs34316627	1.00[ASN][1000 genomes]
rs34529833	1.00[ASN][1000 genomes]
rs34724169	1.00[ASN][1000 genomes]
rs34747259	1.00[ASN][1000 genomes]
rs34942135	1.00[ASN][1000 genomes]
rs35356792	1.00[ASN][1000 genomes]
rs35591322	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888888	1.00[ASN][1000 genomes]
rs35904532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089907	1.00[ASN][1000 genomes]
rs382838	1.00[ASN][1000 genomes]
rs436426	1.00[ASN][1000 genomes]
rs557496	1.00[ASN][1000 genomes]
rs58067500	1.00[ASN][1000 genomes]
rs71358875	1.00[ASN][1000 genomes]
rs71358876	1.00[ASN][1000 genomes]
rs71358877	1.00[ASN][1000 genomes]
rs71358878	1.00[ASN][1000 genomes]
rs71358879	1.00[ASN][1000 genomes]
rs71358884	1.00[ASN][1000 genomes]
rs7252479	1.00[ASN][1000 genomes]
rs7257824	1.00[ASN][1000 genomes]
rs73578236	1.00[ASN][1000 genomes]
rs73578252	1.00[ASN][1000 genomes]
rs8104197	1.00[ASN][1000 genomes]
rs811920	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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
7	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
8	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1058567	chr19:52992455-53021505	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52994200-52997200	ZNF genes & repeats	Ovary	ovary
2	chr19:52994600-52996400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:52994600-52999400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:52994800-52996600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:52994800-52997000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr19:52994800-52997200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:52994800-52997600	ZNF genes & repeats	Fetal Stomach	stomach
8	chr19:52995200-52997200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:52995400-52996000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:52995400-52996800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:52995400-52996800	ZNF genes & repeats	Left Ventricle	heart
12	chr19:52995400-52997000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr19:52995400-52997200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:52995400-52997200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:52995400-52997200	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr19:52995400-52997400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:52995600-52996000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:52995600-52996000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:52995600-52996400	Active TSS	Primary T cells from cord blood	blood
20	chr19:52995600-52996400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
21	chr19:52995600-52996600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:52995600-52996600	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr19:52995600-52997000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:52995600-52997000	ZNF genes & repeats	Esophagus	oesophagus
25	chr19:52995600-52997200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr19:52995600-52997200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr19:52995600-52997200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:52995600-52997200	ZNF genes & repeats	Pancreas	Pancrea
29	chr19:52995600-52997400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:52995600-52997400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:52995800-52996000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr19:52995800-52996200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:52995800-52996200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr19:52995800-52996200	Active TSS	Aorta	Aorta
35	chr19:52995800-52996200	Active TSS	Fetal Muscle Leg	muscle
36	chr19:52995800-52996400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:52995800-52996400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr19:52995800-52996600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr19:52995800-52996600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr19:52995800-52996600	Active TSS	Right Ventricle	heart
41	chr19:52995800-52996600	Active TSS	Dnd41	blood
42	chr19:52995800-52996800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:52995800-52996800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
44	chr19:52995800-52996800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr19:52995800-52996800	Active TSS	Colon Smooth Muscle	Colon
46	chr19:52995800-52996800	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:52995800-52996800	Active TSS	Osteobl	bone
48	chr19:52995800-52997000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood

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