Variant report

Variant	rs1077994
Chromosome Location	chr19:38864699-38864700
allele	A/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	POLR2A	chr19:38864672-38866574	PBDE	blood:	n/a	n/a
2	POLR2A	chr19:38864697-38866015	GM12892	blood:	n/a	n/a
3	MAX	chr19:38864380-38866330	A549	lung:	n/a	n/a
4	ATF3	chr19:38864686-38866133	A549	lung:	n/a	n/a
5	EP300	chr19:38864671-38865792	K562	blood:	n/a	chr19:38865193-38865200
6	POLR2A	chr19:38864690-38866384	GM12892	blood:	n/a	n/a
7	GATA3	chr19:38864694-38866413	A549	lung:	n/a	n/a
8	POLR2A	chr19:38864449-38866103	HepG2	liver:	n/a	n/a
9	PML	chr19:38864671-38866014	GM12878	blood:	n/a	n/a
10	MTA3	chr19:38864661-38866347	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr19:38864674-38866120	MCF-7	breast:	n/a	n/a
12	TCF12	chr19:38864539-38866641	A549	lung:	n/a	chr19:38866085-38866093
13	POLR2A	chr19:38864668-38866834	K562	blood:	n/a	n/a
14	EGR1	chr19:38864697-38866072	HCT-116	colon:	n/a	chr19:38865636-38865650 chr19:38865956-38865969 chr19:38865959-38865968
15	ESRRA	chr19:38864097-38866266	GM12878	blood:	n/a	n/a
16	SIX5	chr19:38864673-38865790	A549	lung:	n/a	n/a
17	POLR2A	chr19:38864594-38865911	PFSK-1	brain:	n/a	n/a
18	SP1	chr19:38864483-38866037	A549	lung:	n/a	n/a
19	MAX	chr19:38864575-38866183	K562	blood:	n/a	n/a
20	POLR2A	chr19:38864657-38866462	GM12878	blood:	n/a	n/a
21	GABPA	chr19:38864699-38865952	MCF-7	breast:	n/a	n/a
22	YY1	chr19:38864477-38866253	A549	lung:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38866231-38866245 chr19:38865200-38865222
23	SIX5	chr19:38864550-38866204	A549	lung:	n/a	n/a
24	SP1	chr19:38864655-38865983	A549	lung:	n/a	n/a
25	TCF12	chr19:38864697-38865973	MCF-7	breast:	n/a	n/a
26	POLR2A	chr19:38864659-38865845	U87	brain:	n/a	n/a
27	HCFC1	chr19:38864615-38865995	Hela-S3	cervix:	n/a	n/a
28	REST	chr19:38864130-38866180	A549	lung:	n/a	chr19:38865066-38865075 chr19:38864254-38864262
29	MXI1	chr19:38864586-38867349	SK-N-SH	brain:	n/a	n/a
30	EP300	chr19:38864666-38866170	A549	lung:	n/a	chr19:38865193-38865200
31	ETS1	chr19:38864547-38865965	A549	lung:	n/a	chr19:38865189-38865205 chr19:38865192-38865201 chr19:38865192-38865201 chr19:38865190-38865201 chr19:38865190-38865200 chr19:38865192-38865201 chr19:38865192-38865201 chr19:38865192-38865201 chr19:38865192-38865201
32	EP300	chr19:38864652-38865812	A549	lung:	n/a	chr19:38865193-38865200
33	POLR2A	chr19:38864698-38865793	HUVEC	blood vessel:	n/a	n/a
34	SIN3AK20	chr19:38864675-38866459	A549	lung:	n/a	n/a
35	YY1	chr19:38864600-38865962	K562	blood:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
36	YY1	chr19:38864672-38865888	SK-N-SH	brain:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
37	YY1	chr19:38864592-38866195	SK-N-SH	brain:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
38	BCL3	chr19:38864664-38865844	A549	lung:	n/a	chr19:38865192-38865201
39	YY1	chr19:38864506-38865906	A549	lung:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
40	TCF12	chr19:38864691-38866029	A549	lung:	n/a	n/a
41	TBL1XR1	chr19:38864684-38865624	K562	blood:	n/a	n/a
42	GABPA	chr19:38864648-38865990	A549	lung:	n/a	n/a
43	REST	chr19:38864537-38866326	H1-neurons	neurons:	n/a	chr19:38865066-38865075

No.	Distal block	Cell Line	Cell type
1	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
2	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
3	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
4	chr19:38809437..38811955-chr19:38862671..38865032,2	K562	blood:
5	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
6	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
7	chr19:38704545..38706333-chr19:38863890..38866208,2	K562	blood:
8	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
9	chr19:38753811..38757692-chr19:38863788..38867160,7	MCF-7	breast:
10	chr19:38806279..38807928-chr19:38863720..38866328,2	K562	blood:
11	chr19:38863925..38865445-chr7:7605772..7607416,2	MCF-7	breast:
12	chr19:38719001..38721753-chr19:38863587..38865113,2	K562	blood:
13	chr19:38747172..38749523-chr19:38863877..38866599,2	K562	blood:
14	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
15	chr19:38825879..38826868-chr19:38864639..38865169,2	K562	blood:
16	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
17	chr19:38825004..38828693-chr19:38863595..38867873,9	K562	blood:
18	chr19:38851531..38855576-chr19:38863499..38866575,5	MCF-7	breast:
19	chr19:38711690..38716111-chr19:38864242..38867673,4	MCF-7	breast:
20	chr19:38864558..38865474-chr5:133860937..133861908,2	Hela-S3	cervix:

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000099337	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000238838	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000043143	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000266963	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12608599	0.85[ASN][1000 genomes]
rs12608644	0.81[ASN][1000 genomes]
rs12608722	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12609258	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12610650	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2074982	0.82[ASN][1000 genomes]
rs2302186	0.86[ASN][1000 genomes]
rs2302227	0.82[ASN][1000 genomes]
rs3745958	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3745959	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3948666	0.85[ASN][1000 genomes]
rs45485196	0.85[ASN][1000 genomes]
rs56854837	0.82[ASN][1000 genomes]
rs57146784	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58462889	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6508790	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72480720	0.85[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38861200-38865000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:38864000-38866800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38864200-38864800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:38864400-38864800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:38864400-38864800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:38864400-38864800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:38864400-38864800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:38864400-38864800	Enhancers	Fetal Intestine Small	intestine
9	chr19:38864400-38864800	Enhancers	Placenta	Placenta
10	chr19:38864400-38865000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:38864400-38865000	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr19:38864400-38865000	Flanking Active TSS	Dnd41	blood
13	chr19:38864400-38865000	Flanking Active TSS	K562	blood
14	chr19:38864400-38866200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:38864600-38864800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr19:38864600-38864800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38864600-38864800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:38864600-38864800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:38864600-38864800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:38864600-38864800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:38864600-38864800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:38864600-38864800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr19:38864600-38864800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr19:38864600-38864800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr19:38864600-38864800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr19:38864600-38864800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:38864600-38864800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr19:38864600-38864800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:38864600-38864800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:38864600-38864800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr19:38864600-38864800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr19:38864600-38864800	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr19:38864600-38864800	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr19:38864600-38864800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr19:38864600-38864800	Flanking Active TSS	Colonic Mucosa	Colon
36	chr19:38864600-38864800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr19:38864600-38864800	Flanking Active TSS	Fetal Brain Female	brain
38	chr19:38864600-38864800	Enhancers	Fetal Heart	heart
39	chr19:38864600-38864800	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr19:38864600-38864800	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr19:38864600-38864800	Enhancers	Gastric	stomach
42	chr19:38864600-38864800	Enhancers	Pancreas	Pancrea
43	chr19:38864600-38864800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:38864600-38864800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr19:38864600-38864800	Enhancers	Right Ventricle	heart
46	chr19:38864600-38864800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr19:38864600-38864800	Enhancers	HMEC	breast
48	chr19:38864600-38864800	Active TSS	NHEK	skin
49	chr19:38864600-38865000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr19:38864600-38865000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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