Variant report

Variant	rs28364793
Chromosome Location	chr19:42722068-42722069
allele	A/G
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	PML	chr19:42721464-42722461	K562	blood:	n/a	n/a
2	CTCF	chr19:42721920-42722070	SK-N-SH_RA	brain:	n/a	n/a
3	TAF1	chr19:42720780-42722397	H1-hESC	embryonic stem cell:	n/a	n/a
4	NRF1	chr19:42721683-42722236	GM12878	blood:	n/a	chr19:42722017-42722028 chr19:42721929-42721943 chr19:42721931-42721940 chr19:42721926-42721940 chr19:42721929-42721938 chr19:42722019-42722028 chr19:42721929-42721940 chr19:42722017-42722028 chr19:42722014-42722028 chr19:42721708-42721717 chr19:42722017-42722031
5	CTCF	chr19:42722058-42722076	K562	blood:	n/a	n/a
6	JUND	chr19:42720785-42722359	A549	lung:	n/a	chr19:42722094-42722102 chr19:42721713-42721722
7	FOS	chr19:42721799-42722249	MCF10A-Er-Src	breast:	n/a	chr19:42722094-42722102
8	REST	chr19:42721226-42722781	A549	lung:	n/a	n/a
9	CBX3	chr19:42721483-42722677	K562	blood:	n/a	n/a
10	TCF12	chr19:42721416-42722379	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:42720699-42722341	GM12878	blood:	n/a	n/a
12	EGR1	chr19:42721999-42723054	K562	blood:	n/a	chr19:42722379-42722392 chr19:42722393-42722406 chr19:42722374-42722396 chr19:42722796-42722809 chr19:42722394-42722403 chr19:42722382-42722392 chr19:42722394-42722404 chr19:42722795-42722810 chr19:42722018-42722027 chr19:42722393-42722406 chr19:42722797-42722808 chr19:42722796-42722809 chr19:42722795-42722809 chr19:42722796-42722809 chr19:42722797-42722806 chr19:42722393-42722406 chr19:42722379-42722392 chr19:42722392-42722407 chr19:42722378-42722393 chr19:42722797-42722807
13	THAP1	chr19:42721831-42722222	K562	blood:	n/a	n/a
14	CTCF	chr19:42721920-42722070	GM12871	blood:	n/a	n/a
15	POLR2A	chr19:42721601-42722387	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:42721653-42722386	GM12891	blood:	n/a	n/a
17	FOS	chr19:42721752-42722239	MCF10A-Er-Src	breast:	n/a	chr19:42722094-42722102
18	FOS	chr19:42721800-42722318	MCF10A-Er-Src	breast:	n/a	chr19:42722094-42722102
19	CTCF	chr19:42721940-42722090	SAEC	small airway:	n/a	n/a
20	FOSL2	chr19:42721222-42722678	A549	lung:	n/a	chr19:42722094-42722102 chr19:42722380-42722389 chr19:42722379-42722388 chr19:42721713-42721722 chr19:42722410-42722419
21	MYC	chr19:42721969-42722178	K562	blood:	n/a	n/a
22	POLR2A	chr19:42721371-42722454	GM18526	blood:	n/a	n/a
23	HEY1	chr19:42721371-42722377	HepG2	liver:	n/a	n/a
24	CTCF	chr19:42722000-42722150	AG10803	skin:	n/a	n/a
25	ELF1	chr19:42721596-42722366	MCF-7	breast:	n/a	n/a
26	POLR2A	chr19:42721497-42722565	GM12878	blood:	n/a	n/a
27	UBTF	chr19:42720660-42722365	K562	blood:	n/a	n/a
28	JUND	chr19:42720969-42722213	H1-hESC	embryonic stem cell:	n/a	chr19:42722094-42722102 chr19:42721713-42721722
29	NRF1	chr19:42721739-42722214	Hela-S3	cervix:	n/a	chr19:42722017-42722028 chr19:42721929-42721943 chr19:42721931-42721940 chr19:42721926-42721940 chr19:42721929-42721938 chr19:42722019-42722028 chr19:42721929-42721940 chr19:42722017-42722028 chr19:42722014-42722028 chr19:42722017-42722031
30	GABPA	chr19:42721577-42722430	A549	lung:	n/a	chr19:42721929-42721943 chr19:42721931-42721940 chr19:42721926-42721940 chr19:42721929-42721938 chr19:42722019-42722028 chr19:42721929-42721940 chr19:42722017-42722028 chr19:42722014-42722028 chr19:42721708-42721717 chr19:42722017-42722031
31	ELF1	chr19:42721690-42722362	K562	blood:	n/a	n/a
32	RFX5	chr19:42721725-42722190	HepG2	liver:	n/a	n/a
33	TAF1	chr19:42721675-42722374	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:42721562-42722403	U87	brain:	n/a	n/a
35	PML	chr19:42721532-42722573	GM12878	blood:	n/a	n/a
36	CTCF	chr19:42721992-42722099	MCF-7	breast:	n/a	n/a
37	CUX1	chr19:42721798-42722272	GM12878	blood:	n/a	n/a
38	EP300	chr19:42721783-42722307	K562	blood:	n/a	n/a
39	MAX	chr19:42720549-42723142	K562	blood:	n/a	n/a
40	TAF1	chr19:42721938-42722224	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr19:42721587-42722288	HepG2	liver:	n/a	n/a
42	ZNF143	chr19:42721806-42722199	GM12878	blood:	n/a	chr19:42722103-42722121
43	USF1	chr19:42721752-42722310	A549	lung:	n/a	n/a
44	SIX5	chr19:42721029-42722627	A549	lung:	n/a	n/a
45	POLR2A	chr19:42720631-42723063	K562	blood:	n/a	n/a
46	POLR2A	chr19:42721494-42722335	HepG2	liver:	n/a	n/a
47	MAX	chr19:42721518-42722142	HepG2	liver:	n/a	n/a
48	CTCF	chr19:42721900-42722228	GM12878	blood:	n/a	n/a
49	MYC	chr19:42720895-42722887	K562	blood:	n/a	n/a
50	BATF	chr19:42721995-42722371	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42722032-42722082	AG04450	lung:	fetal
2	chr19:42722068-42722118	HepG2	liver:	n/a
3	chr19:42722068-42722118	AoSMC	blood vessel:	n/a
4	chr19:42722068-42722118	GM19239	blood:	n/a
5	chr19:42722032-42722082	NHBE	bronchial:	n/a
6	chr19:42722068-42722118	NHBE	bronchial:	n/a
7	chr19:42722068-42722118	GM12878	blood:	n/a
8	chr19:42722068-42722118	AG09319	gingival:	n/a
9	chr19:42722032-42722082	Hela-S3	cervix:	n/a
10	chr19:42722068-42722118	HPAEpiC	pulmonary alveolar:	n/a
11	chr19:42722032-42722082	HL-60	blood:	n/a
12	chr19:42722068-42722118	PFSK-1	brain:	n/a
13	chr19:42722032-42722082	Caco-2	colon:	n/a
14	chr19:42722068-42722118	K562	blood:	n/a
15	chr19:42722068-42722118	PrEC	prostate:	n/a
16	chr19:42722068-42722118	GM12892	blood:	n/a
17	chr19:42722032-42722082	RPTEC	kidney:	n/a
18	chr19:42722068-42722118	IMR90	lung:	fetal
19	chr19:42722032-42722082	K562	blood:	n/a
20	chr19:42722068-42722118	ECC-1	luminal epithelium:	n/a
21	chr19:42722032-42722082	T-47D	breast:	n/a
22	chr19:42722032-42722082	HepG2	liver:	n/a
23	chr19:42722068-42722118	Hepatocyte	liver:	n/a
24	chr19:42722032-42722082	SKMC	muscle:	n/a
25	chr19:42722032-42722082	NHDF-neo	bronchial:	n/a
26	chr19:42722032-42722082	HMEC	breast:	n/a
27	chr19:42722032-42722082	GM19239	blood:	n/a
28	chr19:42722032-42722082	HRPEpiC	eye:	n/a
29	chr19:42722032-42722082	HEEpiC	esophagus:	n/a
30	chr19:42722068-42722118	HCT-116	colon:	n/a
31	chr19:42722068-42722118	Caco-2	colon:	n/a
32	chr19:42722032-42722082	GM12878	blood:	n/a
33	chr19:42722068-42722118	AG04450	lung:	fetal
34	chr19:42722068-42722118	HMEC	breast:	n/a
35	chr19:42722068-42722118	HUVEC	blood vessel:	n/a
36	chr19:42722068-42722118	SK-N-SH	brain:	n/a
37	chr19:42722068-42722118	CMK	blood:	n/a
38	chr19:42722032-42722082	HIPEpiC	eye:	n/a
39	chr19:42722068-42722118	T-47D	breast:	n/a
40	chr19:42722068-42722118	H1-hESC	embryonic stem cell:	embryo
41	chr19:42722032-42722082	SAEC	small airway:	n/a
42	chr19:42722032-42722082	AG09309	skin:	n/a
43	chr19:42722032-42722082	NB4	blood:	n/a
44	chr19:42722068-42722118	AG04449	skin:	fetal
45	chr19:42722068-42722118	HCM	heart:	n/a
46	chr19:42722068-42722118	Hela-S3	cervix:	n/a
47	chr19:42722068-42722118	NT2-D1	testis:	n/a
48	chr19:42722068-42722118	HCPEpiC	choroid plexus:	n/a
49	chr19:42722032-42722082	Hepatocyte	liver:	n/a
50	chr19:42722032-42722082	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42720551..42722123-chr19:42758184..42760229,2	MCF-7	breast:
2	chr19:42720188..42722079-chr19:42829743..42831592,2	K562	blood:
3	chr19:42720362..42722122-chr19:42805424..42807081,2	K562	blood:
4	chr19:42634645..42637332-chr19:42721658..42723900,2	K562	blood:
5	chr19:42720002..42723178-chr19:42782377..42785942,3	MCF-7	breast:
6	chr19:42721143..42723529-chr19:42724223..42726542,2	MCF-7	breast:
7	chr19:42636373..42638915-chr19:42720548..42722250,2	K562	blood:
8	chr19:42720843..42724936-chr19:42805318..42808035,4	MCF-7	breast:
9	chr19:42578256..42580709-chr19:42719856..42723017,3	MCF-7	breast:
10	chr19:42720638..42724432-chr19:42771891..42775014,4	MCF-7	breast:
11	chr19:42719158..42725942-chr19:42744280..42751391,14	MCF-7	breast:
12	chr19:42619821..42622788-chr19:42721152..42723229,2	K562	blood:

Variant related genes	Relation type
DEDD2	TF binding region
ZNF526	TF binding region
DEDD2	CpG island
ZNF526	CpG island
ENSG00000204957	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000028277	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000105429	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000268643	Chromatin interaction
ENSG00000254887	Chromatin interaction
ENSG00000167625	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11668239	1.00[LWK][hapmap]
rs11671088	1.00[LWK][hapmap]
rs12460885	1.00[LWK][hapmap]
rs12610116	1.00[LWK][hapmap]
rs12978003	1.00[LWK][hapmap]
rs12985559	1.00[LWK][hapmap]
rs2241563	0.80[JPT][hapmap]
rs2304211	1.00[LWK][hapmap]
rs34343924	1.00[LWK][hapmap]
rs3745226	1.00[LWK][hapmap]
rs7254227	1.00[LWK][hapmap]
rs9676263	1.00[LWK][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	nsv961292	chr19:42710814-42734591	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 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	chr19:42719600-42722400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:42720000-42722200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:42720400-42722200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:42720400-42722400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr19:42720600-42722200	Active TSS	Fetal Intestine Large	intestine
6	chr19:42720600-42722200	Active TSS	Hela-S3	cervix
7	chr19:42720600-42722400	Active TSS	Ovary	ovary
8	chr19:42720800-42722200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:42720800-42722200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:42720800-42722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:42720800-42722200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:42720800-42722200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:42720800-42722200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:42720800-42722200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:42720800-42722200	Active TSS	Primary monocytes fromperipheralblood	blood
16	chr19:42720800-42722200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr19:42720800-42722200	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:42720800-42722200	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr19:42720800-42722200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr19:42720800-42722200	Active TSS	Brain Anterior Caudate	brain
21	chr19:42720800-42722200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:42720800-42722200	Active TSS	Duodenum Mucosa	Duodenum
23	chr19:42720800-42722200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:42720800-42722200	Active TSS	Fetal Kidney	kidney
25	chr19:42720800-42722200	Active TSS	Placenta	Placenta
26	chr19:42720800-42722200	Active TSS	Gastric	stomach
27	chr19:42720800-42722200	Active TSS	Stomach Mucosa	stomach
28	chr19:42720800-42722200	Active TSS	GM12878-XiMat	blood
29	chr19:42720800-42722200	Active TSS	K562	blood
30	chr19:42720800-42722200	Active TSS	NHDF-Ad	bronchial
31	chr19:42720800-42722200	Active TSS	NHEK	skin
32	chr19:42720800-42722200	Active TSS	NHLF	lung
33	chr19:42720800-42722200	Active TSS	Osteobl	bone
34	chr19:42720800-42722400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr19:42720800-42722400	Active TSS	Colon Smooth Muscle	Colon
36	chr19:42720800-42722400	Active TSS	Fetal Brain Female	brain
37	chr19:42720800-42722400	Active TSS	HSMMtube	muscle
38	chr19:42720800-42722600	Active TSS	HSMM	muscle
39	chr19:42720800-42725200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:42721000-42722200	Active TSS	Primary T cells from cord blood	blood
41	chr19:42721000-42722200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:42721000-42722200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:42721000-42722200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:42721000-42722200	Active TSS	Brain Hippocampus Middle	brain
45	chr19:42721000-42722200	Active TSS	Brain Substantia Nigra	brain
46	chr19:42721000-42722200	Active TSS	Fetal Lung	lung
47	chr19:42721000-42722200	Active TSS	Left Ventricle	heart
48	chr19:42721000-42722200	Active TSS	Pancreas	Pancrea
49	chr19:42721000-42722200	Active TSS	Psoas Muscle	Psoas
50	chr19:42721000-42722200	Active TSS	Right Ventricle	heart

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