Variant report

Variant	rs7258644
Chromosome Location	chr19:40873177-40873178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:40872553-40873184	H1-hESC	embryonic stem cell:	n/a	n/a
2	RFX5	chr19:40872128-40873193	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:40872863-40873179	K562	blood:	n/a	n/a
4	CTCF	chr19:40873020-40873250	HL-60	blood:	n/a	n/a
5	REST	chr19:40871135-40873268	H1-neurons	neurons:	n/a	chr19:40871712-40871725 chr19:40871468-40871477
6	SIN3A	chr19:40871833-40873293	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:40872447-40873277	H1-neurons	neurons:	n/a	n/a
8	BACH1	chr19:40872521-40873192	H1-hESC	embryonic stem cell:	n/a	n/a
9	EGR1	chr19:40872703-40873218	K562	blood:	n/a	n/a
10	RFX5	chr19:40870879-40873177	SK-N-SH	brain:	n/a	n/a
11	CREB1	chr19:40872466-40873280	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr19:40872871-40873384	K562	blood:	n/a	n/a
13	CTCF	chr19:40872837-40873290	K562	blood:	n/a	n/a
14	RFX5	chr19:40871873-40873323	IMR90	lung:	n/a	n/a
15	BCL3	chr19:40871966-40873201	A549	lung:	n/a	n/a

No data

(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
ENSG00000160392	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs61156500	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7258698	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	chr19:40871400-40873400	Active TSS	Brain Anterior Caudate	brain
11	chr19:40871400-40878000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:40871400-40880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:40871600-40880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:40871600-40881800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:40872000-40873200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:40872000-40877000	Weak transcription	Small Intestine	intestine
17	chr19:40872000-40878800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:40872000-40880200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:40872200-40873200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr19:40872200-40873200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:40872200-40873200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:40872200-40873200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:40872200-40873400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
24	chr19:40872200-40876800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr19:40872200-40880400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:40872200-40880800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:40872200-40880800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr19:40872200-40881600	Weak transcription	GM12878-XiMat	blood
29	chr19:40872200-40887000	Strong transcription	Liver	Liver
30	chr19:40872200-40887400	Weak transcription	Primary B cells from cord blood	blood
31	chr19:40872200-40887400	Weak transcription	Stomach Mucosa	stomach
32	chr19:40872400-40873200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:40872400-40873200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:40872400-40873200	Genic enhancers	Placenta	Placenta
35	chr19:40872400-40873800	Enhancers	Fetal Heart	heart
36	chr19:40872400-40873800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr19:40872400-40874400	Strong transcription	Thymus	Thymus
38	chr19:40872400-40875200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:40872400-40876600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:40872400-40877200	Weak transcription	NHEK	skin
41	chr19:40872400-40878000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:40872400-40880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:40872400-40880400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:40872400-40881200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:40872400-40881400	Strong transcription	Ovary	ovary
46	chr19:40872400-40885600	Weak transcription	NHDF-Ad	bronchial
47	chr19:40872400-40886200	Weak transcription	HUVEC	blood vessel
48	chr19:40872600-40873200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr19:40872600-40873200	Genic enhancers	A549	lung
50	chr19:40872600-40873600	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain

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