Variant report

Variant	rs7258698
Chromosome Location	chr19:40872964-40872965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:40872960-40873110	HBMEC	blood vessel:	n/a	n/a
2	CREB1	chr19:40872553-40873153	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr19:40872564-40873062	K562	blood:	n/a	n/a
4	ZNF263	chr19:40872635-40873142	HEK293-T-REx	kidney:	n/a	chr19:40872957-40872978
5	CTCF	chr19:40872880-40873030	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr19:40872726-40873060	K562	blood:	n/a	n/a
7	MXI1	chr19:40872585-40873093	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr19:40872586-40873079	H1-hESC	embryonic stem cell:	n/a	chr19:40872847-40872858
9	CTCF	chr19:40872920-40873070	SK-N-SH_RA	brain:	n/a	n/a
10	SIN3AK20	chr19:40872848-40873138	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:40872240-40873159	H1-neurons	neurons:	n/a	n/a
12	CTCF	chr19:40872908-40873135	K562	blood:	n/a	n/a
13	CTCF	chr19:40872940-40873090	AG04449	skin:	n/a	n/a
14	CTCF	chr19:40872880-40873030	HPAF	blood vessel:	n/a	n/a
15	RAD21	chr19:40872553-40873184	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr19:40872846-40873163	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr19:40872920-40873070	HCPEpiC	choroid plexus:	n/a	n/a
18	MAFK	chr19:40872150-40873001	K562	blood:	n/a	chr19:40872736-40872751
19	CTCF	chr19:40872900-40873050	NHDF-neo	bronchial:	n/a	n/a
20	RFX5	chr19:40872128-40873193	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:40872836-40873099	K562	blood:	n/a	n/a
22	RAD21	chr19:40872851-40873151	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr19:40872917-40873100	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZNF143	chr19:40872725-40873040	H1-hESC	embryonic stem cell:	n/a	n/a
25	EGR1	chr19:40872733-40873160	K562	blood:	n/a	n/a
26	POLR2A	chr19:40872636-40872987	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr19:40872863-40873179	K562	blood:	n/a	n/a
28	TAF1	chr19:40872752-40873043	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIN3AK20	chr19:40872732-40873137	H1-hESC	embryonic stem cell:	n/a	n/a
30	SMC3	chr19:40872957-40873127	K562	blood:	n/a	n/a
31	CTCF	chr19:40872955-40873070	SK-N-SH_RA	brain:	n/a	n/a
32	JUND	chr19:40872579-40873081	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAZ	chr19:40872690-40873165	K562	blood:	n/a	n/a
34	REST	chr19:40871135-40873268	H1-neurons	neurons:	n/a	chr19:40871712-40871725 chr19:40871468-40871477
35	JUND	chr19:40872544-40872997	A549	lung:	n/a	n/a
36	POLR2A	chr19:40872736-40873120	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr19:40872920-40873070	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr19:40872920-40873070	HRE	kidney:	n/a	n/a
39	CHD2	chr19:40872732-40873027	H1-hESC	embryonic stem cell:	n/a	n/a
40	RFX5	chr19:40872550-40873000	K562	blood:	n/a	n/a
41	JUND	chr19:40872605-40873071	K562	blood:	n/a	n/a
42	CTCF	chr19:40872960-40873110	AG04449	skin:	n/a	n/a
43	SIN3A	chr19:40871833-40873293	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr19:40872793-40873162	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr19:40872900-40873050	HRPEpiC	eye:	n/a	n/a
46	CTCF	chr19:40872960-40873110	A549	lung:	n/a	n/a
47	CTCF	chr19:40872940-40873090	BE2_C	brain:	n/a	n/a
48	RCOR1	chr19:40872709-40873157	K562	blood:	n/a	n/a
49	POLR2A	chr19:40872447-40873277	H1-neurons	neurons:	n/a	n/a
50	MAFK	chr19:40872503-40873082	H1-hESC	embryonic stem cell:	n/a	chr19:40872736-40872751

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40872963-40873013	ovcar-3	ovarian:	n/a
2	chr19:40872963-40873013	AoSMC	blood vessel:	n/a
3	chr19:40872963-40873013	Caco-2	colon:	n/a
4	chr19:40872963-40873013	HPAEpiC	pulmonary alveolar:	n/a
5	chr19:40872963-40873013	GM12878	blood:	n/a
6	chr19:40872963-40873013	HCM	heart:	n/a
7	chr19:40872963-40873013	NB4	blood:	n/a
8	chr19:40872963-40873013	Hela-S3	cervix:	n/a
9	chr19:40872963-40873013	BE2_C	brain:	n/a
10	chr19:40872963-40873013	PrEC	prostate:	n/a
11	chr19:40872963-40873013	AG09309	skin:	n/a
12	chr19:40872963-40873013	CMK	blood:	n/a
13	chr19:40872963-40873013	AG04450	lung:	fetal
14	chr19:40872963-40873013	NH-A	brain:	n/a
15	chr19:40872963-40873013	SKMC	muscle:	n/a
16	chr19:40872963-40873013	HL-60	blood:	n/a
17	chr19:40872963-40873013	HRE	kidney:	n/a
18	chr19:40872963-40873013	PANC-1	pancreas:	n/a
19	chr19:40872963-40873013	HIPEpiC	eye:	n/a
20	chr19:40872963-40873013	H1-hESC	embryonic stem cell:	embryo
21	chr19:40872963-40873013	GM19239	blood:	n/a
22	chr19:40872963-40873013	ProgFib	skin:	n/a
23	chr19:40872963-40873013	IMR90	lung:	fetal
24	chr19:40872963-40873013	AG04449	skin:	fetal
25	chr19:40872963-40873013	GM06990	blood:	n/a
26	chr19:40872963-40873013	ECC-1	luminal epithelium:	n/a
27	chr19:40872963-40873013	AG10803	skin:	n/a
28	chr19:40872963-40873013	NHDF-neo	bronchial:	n/a
29	chr19:40872963-40873013	BJ	skin:	n/a
30	chr19:40872963-40873013	SAEC	small airway:	n/a
31	chr19:40872963-40873013	LNCaP	prostate:	n/a
32	chr19:40872963-40873013	Jurkat	blood:	n/a
33	chr19:40872963-40873013	HUVEC	blood vessel:	n/a
34	chr19:40872963-40873013	PFSK-1	brain:	n/a
35	chr19:40872963-40873013	K562	blood:	n/a
36	chr19:40872963-40873013	HAEpiC	amniotic membrane:	n/a
37	chr19:40872963-40873013	HMEC	breast:	n/a
38	chr19:40872963-40873013	SK-N-SH	brain:	n/a
39	chr19:40872963-40873013	MCF-7	breast:	n/a
40	chr19:40872963-40873013	HRPEpiC	eye:	n/a
41	chr19:40872963-40873013	GM12891	blood:	n/a
42	chr19:40872963-40873013	SK-N-SH_RA	brain:	n/a
43	chr19:40872963-40873013	A549	lung:	n/a
44	chr19:40872963-40873013	HEEpiC	esophagus:	n/a
45	chr19:40872963-40873013	T-47D	breast:	n/a
46	chr19:40872963-40873013	HepG2	liver:	n/a
47	chr19:40872963-40873013	HEK293	kidney:	embryo
48	chr19:40872963-40873013	AG09319	gingival:	n/a
49	chr19:40872963-40873013	HCF	heart:	n/a
50	chr19:40872963-40873013	Hepatocyte	liver:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40872773..40875279-chr19:40947114..40949587,2	MCF-7	breast:
2	chr19:40871399..40873177-chr19:40948575..40950979,2	K562	blood:
3	chr19:40858935..40867508-chr19:40870167..40875772,11	K562	blood:
4	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
5	chr19:40871827..40874303-chr19:40947667..40950023,2	MCF-7	breast:
6	chr19:40872240..40873973-chr19:40882953..40885415,2	MCF-7	breast:
7	chr19:40871826..40875683-chr19:40883249..40885550,3	MCF-7	breast:

No data

Variant related genes	Relation type
PLD3	TF binding region
PLD3	CpG island
ENSG00000268366	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11670988	0.83[CHD][hapmap]
rs61156500	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7258644	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40855600-40873400	Weak transcription	Aorta	Aorta
2	chr19:40855600-40875800	Weak transcription	HSMMtube	muscle
3	chr19:40856600-40873600	Weak transcription	Psoas Muscle	Psoas
4	chr19:40864000-40884400	Weak transcription	HepG2	liver
5	chr19:40866000-40877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:40869400-40878800	Weak transcription	HSMM	muscle
7	chr19:40869800-40880200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:40871000-40873400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr19:40871000-40873600	Weak transcription	Dnd41	blood
10	chr19:40871400-40873000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:40871400-40873400	Active TSS	Brain Anterior Caudate	brain
12	chr19:40871400-40878000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:40871400-40880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:40871600-40873000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:40871600-40873000	Weak transcription	Primary T cells from cord blood	blood
16	chr19:40871600-40880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:40871600-40881800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:40872000-40873000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:40872000-40873000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:40872000-40873000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:40872000-40873000	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr19:40872000-40873000	Flanking Active TSS	K562	blood
23	chr19:40872000-40873000	Flanking Active TSS	NH-A	brain
24	chr19:40872000-40873200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr19:40872000-40877000	Weak transcription	Small Intestine	intestine
26	chr19:40872000-40878800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:40872000-40880200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:40872200-40873000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:40872200-40873000	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr19:40872200-40873000	Genic enhancers	Lung	lung
31	chr19:40872200-40873000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr19:40872200-40873200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr19:40872200-40873200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:40872200-40873200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr19:40872200-40873200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:40872200-40873400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr19:40872200-40876800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:40872200-40880400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr19:40872200-40880800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:40872200-40880800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:40872200-40881600	Weak transcription	GM12878-XiMat	blood
42	chr19:40872200-40887000	Strong transcription	Liver	Liver
43	chr19:40872200-40887400	Weak transcription	Primary B cells from cord blood	blood
44	chr19:40872200-40887400	Weak transcription	Stomach Mucosa	stomach
45	chr19:40872400-40873000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:40872400-40873000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:40872400-40873000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:40872400-40873000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:40872400-40873000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:40872400-40873000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin

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