Variant report

Variant	rs2230765
Chromosome Location	chr19:39923985-39923986
allele	C/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	EP300	chr19:39923741-39924056	T-47D	breast:	n/a	n/a
2	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
3	PML	chr19:39923806-39924416	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
6	JUND	chr19:39920490-39925442	A549	lung:	n/a	chr19:39921458-39921466 chr19:39924892-39924906 chr19:39921457-39921466 chr19:39921456-39921467 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467 chr19:39922370-39922379 chr19:39922373-39922382 chr19:39922371-39922380
7	POLR2A	chr19:39920391-39924937	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:39922557-39925396	K562	blood:	n/a	n/a
9	ZBTB33	chr19:39923756-39924473	K562	blood:	n/a	n/a
10	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
11	CHD1	chr19:39922434-39927571	IMR90	lung:	n/a	chr19:39927410-39927420
12	POLR2A	chr19:39923897-39924034	A549	lung:	n/a	n/a
13	TCF7L2	chr19:39923094-39925387	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:39920942-39925617	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:39920975-39927064	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:39923951-39924254	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr19:39920712-39925660	IMR90	lung:	n/a	n/a
19	POLR2A	chr19:39922355-39925341	SK-N-SH	brain:	n/a	n/a
20	BCL3	chr19:39922482-39925602	A549	lung:	n/a	chr19:39924869-39924878
21	POLR2A	chr19:39921015-39927381	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:39921127-39925489	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:39923863-39925119	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:39922588-39925489	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:39922723-39925532	K562	blood:	n/a	n/a
26	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
27	POLR2A	chr19:39923976-39924498	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:39920992-39925485	GM12891	blood:	n/a	n/a
29	REST	chr19:39920516-39925106	PANC-1	pancreas:	n/a	chr19:39924867-39924880
30	POLR2A	chr19:39921169-39925654	K562	blood:	n/a	n/a
31	REST	chr19:39923831-39924081	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:39922383-39925441	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:39921059-39925766	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
35	POLR2A	chr19:39921027-39924615	A549	lung:	n/a	n/a
36	ETS1	chr19:39922892-39923999	A549	lung:	n/a	n/a
37	POLR2A	chr19:39921064-39925450	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr19:39923887-39924589	A549	lung:	n/a	n/a
39	POLR2A	chr19:39922700-39925056	GM18505	blood:	n/a	n/a
40	SIN3AK20	chr19:39923853-39924068	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr19:39923811-39924128	T-47D	breast:	n/a	n/a
42	MTA3	chr19:39922510-39924001	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:39922720-39925026	GM19193	blood:	n/a	n/a
44	POLR2A	chr19:39921143-39925465	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:39922601-39925454	GM12891	blood:	n/a	n/a
46	POLR2A	chr19:39922392-39925452	H1-hESC	embryonic stem cell:	n/a	n/a
47	GATA3	chr19:39923831-39924061	T-47D	breast:	n/a	n/a
48	SIN3AK20	chr19:39920798-39927887	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr19:39920903-39927409	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr19:39920869-39927284	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39830753..39833020-chr19:39922309..39924224,2	K562	blood:
2	chr19:39875302..39877706-chr19:39923653..39926638,3	MCF-7	breast:
3	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
4	chr17:7475764..7476400-chr19:39923946..39924715,2	Hela-S3	cervix:
5	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
6	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000269246	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000161960	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10408589	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409917	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10410092	0.92[AFR][1000 genomes]
rs10413140	1.00[EUR][1000 genomes]
rs10413673	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415077	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415279	1.00[EUR][1000 genomes]
rs13346052	1.00[EUR][1000 genomes]
rs4100178	1.00[EUR][1000 genomes]
rs6508847	1.00[EUR][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	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
3	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
6	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 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	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39919600-39925000	Weak transcription	Right Atrium	heart
3	chr19:39919800-39924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39920000-39924200	Weak transcription	Fetal Heart	heart
5	chr19:39921200-39924600	Strong transcription	Brain Germinal Matrix	brain
6	chr19:39921200-39924800	Strong transcription	Brain Hippocampus Middle	brain
7	chr19:39921400-39924200	Strong transcription	Colon Smooth Muscle	Colon
8	chr19:39921600-39924200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:39921600-39924800	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr19:39921600-39925200	Strong transcription	Thymus	Thymus
11	chr19:39921600-39925600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:39921800-39924200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:39921800-39924200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:39921800-39924600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:39921800-39924600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:39921800-39924600	Strong transcription	Fetal Stomach	stomach
17	chr19:39922000-39924000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr19:39922000-39924200	Strong transcription	Fetal Muscle Leg	muscle
19	chr19:39922000-39924200	Strong transcription	Right Ventricle	heart
20	chr19:39922000-39924400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:39922000-39924800	Strong transcription	Fetal Intestine Small	intestine
22	chr19:39922000-39924800	Weak transcription	Stomach Mucosa	stomach
23	chr19:39922000-39925200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:39922200-39924200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:39922200-39924200	Strong transcription	Adipose Nuclei	Adipose
26	chr19:39922200-39924200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr19:39922200-39924400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:39922200-39924400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:39922200-39924400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:39922200-39924600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr19:39922200-39924800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:39922200-39924800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:39922400-39924400	Strong transcription	Placenta	Placenta
34	chr19:39922400-39924400	Strong transcription	Fetal Thymus	thymus
35	chr19:39922600-39924600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:39922600-39924600	Strong transcription	Liver	Liver
37	chr19:39922600-39925200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:39922800-39924000	Strong transcription	Lung	lung
39	chr19:39922800-39924400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:39922800-39924400	Strong transcription	Psoas Muscle	Psoas
41	chr19:39922800-39924600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:39922800-39924600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:39922800-39924600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr19:39922800-39924600	Strong transcription	Osteobl	bone
45	chr19:39922800-39924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39922800-39924800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:39922800-39924800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:39922800-39924800	Strong transcription	Fetal Intestine Large	intestine
49	chr19:39922800-39925200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:39923000-39924000	Strong transcription	Brain Anterior Caudate	brain

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