Variant report

Variant	rs55745204
Chromosome Location	chr19:35740806-35740807
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:35740723-35741447	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:35738468-35741259	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr19:35738983-35741180	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:35738488-35740854	HepG2	liver:	n/a	n/a
5	SMARCB1	chr19:35738479-35741061	Hela-S3	cervix:	n/a	n/a
6	SIN3A	chr19:35738415-35740871	H1-hESC	embryonic stem cell:	n/a	chr19:35739308-35739319
7	POLR2A	chr19:35738375-35741593	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:35737830-35741820	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr19:35738258-35740869	H1-hESC	embryonic stem cell:	n/a	chr19:35740222-35740232

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35644198..35645864-chr19:35739143..35741806,2	MCF-7	breast:
2	chr19:35654052..35658593-chr19:35736953..35742683,9	K562	blood:
3	chr19:35738993..35741387-chr19:36004208..36006245,2	MCF-7	breast:
4	chr15:65588204..65590632-chr19:35739036..35741100,2	MCF-7	breast:
5	chr19:35650702..35653470-chr19:35739367..35741084,2	K562	blood:
6	chr19:35740149..35740892-chr21:48055035..48055759,2	Hela-S3	cervix:
7	chr19:35632170..35634028-chr19:35739536..35741421,2	K562	blood:
8	chr19:35627197..35629853-chr19:35739578..35741955,2	K562	blood:
9	chr19:35639021..35648956-chr19:35737438..35742195,14	K562	blood:
10	chr19:35739927..35742259-chr19:35996033..35997931,2	K562	blood:
11	chr19:35604580..35611543-chr19:35737733..35741283,12	MCF-7	breast:
12	chr19:35739540..35741218-chr19:36118965..36121902,2	MCF-7	breast:
13	chr19:35625494..35628326-chr19:35738306..35742693,4	MCF-7	breast:
14	chr19:35723373..35727135-chr19:35736732..35741150,5	MCF-7	breast:
15	chr19:35720837..35725765-chr19:35738586..35741342,4	K562	blood:
16	chr19:35531384..35534577-chr19:35737191..35741282,3	MCF-7	breast:
17	chr19:35519110..35522906-chr19:35737918..35741487,5	MCF-7	breast:
18	chr19:35624985..35627104-chr19:35738782..35741299,2	K562	blood:
19	chr19:35526884..35529258-chr19:35738897..35741083,2	K562	blood:
20	chr19:35644753..35650464-chr19:35737058..35742117,12	K562	blood:
21	chr19:35603872..35607710-chr19:35737437..35742074,6	MCF-7	breast:
22	chr19:35625357..35628180-chr19:35737479..35741018,4	MCF-7	breast:
23	chr12:120729617..120731588-chr19:35739075..35741245,2	MCF-7	breast:
24	chr19:35651223..35652783-chr19:35738946..35741329,2	MCF-7	breast:
25	chr19:35631922..35638346-chr19:35737284..35742337,12	MCF-7	breast:
26	chr19:35739560..35741618-chr19:36133175..36135201,2	K562	blood:
27	chr19:35632170..35634290-chr19:35738915..35741421,3	K562	blood:
28	chr19:35630586..35637861-chr19:35737374..35742554,18	MCF-7	breast:

No data

Variant related genes	Relation type
LSR	TF binding region
ENSG00000266964	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000267874	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000089356	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000105707	Chromatin interaction
ENSG00000105711	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000161249	Chromatin interaction
ENSG00000221946	Chromatin interaction
ENSG00000160310	Chromatin interaction
ENSG00000089327	Chromatin interaction
ENSG00000153902	Chromatin interaction
ENSG00000221857	Chromatin interaction
ENSG00000126254	Chromatin interaction
ENSG00000262497	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10416533	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12459658	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17173026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882695	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2005927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280746	0.92[EUR][1000 genomes]
rs4805116	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4806114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4806115	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4806121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806125	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55863037	0.92[EUR][1000 genomes]
rs55877896	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56002756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66868858	0.92[EUR][1000 genomes]
rs73029949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73045840	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73045852	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73045860	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7508022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking 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	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv978896	chr19:35724047-35748472	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35738000-35741000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:35738200-35741000	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr19:35738200-35741400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:35738400-35741000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:35738400-35741000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:35738400-35741200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:35738400-35741200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:35738600-35741000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:35738600-35741000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:35738600-35741000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:35738600-35741200	Active TSS	Lung	lung
12	chr19:35738800-35741000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr19:35738800-35741000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr19:35738800-35741200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
15	chr19:35739000-35741000	Active TSS	Gastric	stomach
16	chr19:35739400-35741000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:35739400-35741200	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chr19:35739400-35741400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
19	chr19:35739600-35741200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:35740200-35741200	Bivalent Enhancer	Brain Substantia Nigra	brain
21	chr19:35740400-35741000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr19:35740400-35741000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:35740400-35741000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:35740400-35741000	Active TSS	Stomach Mucosa	stomach
25	chr19:35740400-35741200	Flanking Active TSS	Pancreas	Pancrea
26	chr19:35740400-35744600	Weak transcription	Left Ventricle	heart
27	chr19:35740600-35741000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:35740600-35741000	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:35740600-35741000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr19:35740600-35741000	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr19:35740600-35741000	Flanking Active TSS	Colonic Mucosa	Colon
32	chr19:35740600-35741000	Bivalent Enhancer	Spleen	Spleen
33	chr19:35740600-35741000	Active TSS	HepG2	liver
34	chr19:35740600-35741000	Flanking Active TSS	K562	blood
35	chr19:35740600-35741200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:35740600-35741200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:35740600-35741200	Flanking Active TSS	Hela-S3	cervix
38	chr19:35740600-35741400	Flanking Active TSS	Liver	Liver
39	chr19:35740600-35741600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr19:35740600-35745200	Weak transcription	Right Atrium	heart
41	chr19:35740600-35748000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:35740600-35748200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:35740800-35741000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:35740800-35741000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr19:35740800-35741000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:35740800-35741000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:35740800-35741000	Bivalent Enhancer	Brain Anterior Caudate	brain
48	chr19:35740800-35741000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
49	chr19:35740800-35741000	Flanking Active TSS	Fetal Heart	heart
50	chr19:35740800-35741000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon

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