Variant report

Variant	rs7253975
Chromosome Location	chr19:40871790-40871791
allele	C/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	POLR2A	chr19:40871521-40871850	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr19:40871489-40871867	SK-N-SH	brain:	n/a	chr19:40871712-40871725
3	NRF1	chr19:40871512-40871826	Hela-S3	cervix:	n/a	chr19:40871694-40871705 chr19:40871735-40871744
4	POLR2A	chr19:40871446-40871903	HUVEC	blood vessel:	n/a	n/a
5	E2F6	chr19:40871679-40871847	K562	blood:	n/a	chr19:40871735-40871744
6	MAX	chr19:40871657-40872126	K562	blood:	n/a	chr19:40871736-40871746 chr19:40871739-40871749
7	POLR2A	chr19:40871217-40872303	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr19:40871467-40872026	K562	blood:	n/a	n/a
9	POLR2A	chr19:40871469-40871840	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:40871425-40871939	A549	lung:	n/a	n/a
11	TAF1	chr19:40871411-40871987	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr19:40871540-40871882	A549	lung:	n/a	n/a
13	SP1	chr19:40871376-40871901	H1-hESC	embryonic stem cell:	n/a	chr19:40871856-40871870 chr19:40871734-40871748 chr19:40871740-40871754 chr19:40871714-40871726 chr19:40871734-40871743 chr19:40871733-40871745 chr19:40871714-40871726 chr19:40871733-40871745 chr19:40871734-40871744 chr19:40871735-40871744 chr19:40871734-40871744 chr19:40871734-40871743
14	ZBTB7A	chr19:40871505-40872460	K562	blood:	n/a	n/a
15	POLR2A	chr19:40871460-40871841	GM18951	blood:	n/a	n/a
16	POLR2A	chr19:40871267-40872021	U87	brain:	n/a	n/a
17	MAZ	chr19:40871766-40871800	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:40871435-40871882	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr19:40871469-40871883	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:40871259-40872032	HUVEC	blood vessel:	n/a	n/a
21	MAX	chr19:40871453-40871954	ECC-1	luminal epithelium:	n/a	chr19:40871736-40871746 chr19:40871739-40871749
22	IRF1	chr19:40871510-40871868	K562	blood:	n/a	chr19:40871731-40871745 chr19:40871714-40871728
23	POLR2A	chr19:40871283-40872520	K562	blood:	n/a	n/a
24	POLR2A	chr19:40871487-40871832	GM15510	blood:	n/a	n/a
25	MAZ	chr19:40871511-40872313	K562	blood:	n/a	chr19:40871736-40871746 chr19:40871739-40871749
26	POLR2A	chr19:40871299-40871908	HUVEC	blood vessel:	n/a	n/a
27	TAF1	chr19:40871421-40871982	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr19:40871340-40872106	SK-N-SH	brain:	n/a	n/a
29	TAF1	chr19:40871619-40871868	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:40871485-40871811	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr19:40871548-40871864	ProgFib	skin:	n/a	n/a
32	POLR2A	chr19:40871455-40871930	K562	blood:	n/a	n/a
33	POLR2A	chr19:40871429-40871797	GM12891	blood:	n/a	n/a
34	TAF1	chr19:40871354-40872038	H1-neurons	neurons:	n/a	n/a
35	RAD21	chr19:40871439-40871980	SK-N-SH_RA	brain:	n/a	chr19:40871712-40871724
36	POLR2A	chr19:40871443-40871977	Gliobla	brain:	n/a	n/a
37	RUNX3	chr19:40871481-40871858	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:40871447-40871890	K562	blood:	n/a	n/a
39	HMGN3	chr19:40871532-40872198	K562	blood:	n/a	n/a
40	POLR2A	chr19:40871487-40871836	A549	lung:	n/a	n/a
41	POLR2A	chr19:40871504-40871911	K562	blood:	n/a	n/a
42	POLR2A	chr19:40871461-40871835	Raji	blood:	n/a	n/a
43	TBP	chr19:40871463-40871866	K562	blood:	n/a	n/a
44	POLR2A	chr19:40871471-40871831	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:40871450-40871939	K562	blood:	n/a	n/a
46	TAF1	chr19:40871455-40871909	SK-N-SH	brain:	n/a	n/a
47	REST	chr19:40871135-40873268	H1-neurons	neurons:	n/a	chr19:40871712-40871725 chr19:40871468-40871477
48	EGR1	chr19:40871557-40871912	K562	blood:	n/a	chr19:40871737-40871747 chr19:40871736-40871749 chr19:40871734-40871744 chr19:40871735-40871750 chr19:40871736-40871749
49	TBP	chr19:40871504-40871801	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:40871484-40871840	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40870911..40872668-chr19:40875500..40877500,2	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	chr19:40789879..40793059-chr19:40870323..40872928,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-1	chr19:40871460-40871837	NONHSAT066375
2	lnc-PLD3-1	chr19:40871625-40871837	NONHSAT066374

Variant related genes	Relation type
PLD3	TF binding region
ENSG00000268366	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10419783	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3745196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3745197	0.91[ASN][1000 genomes]
rs8103643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8106701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8110995	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	chr19:40855600-40872400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:40855600-40872400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:40855600-40872600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:40855600-40873400	Weak transcription	Aorta	Aorta
5	chr19:40855600-40875800	Weak transcription	HSMMtube	muscle
6	chr19:40856600-40873600	Weak transcription	Psoas Muscle	Psoas
7	chr19:40864000-40884400	Weak transcription	HepG2	liver
8	chr19:40865400-40872000	Weak transcription	Colonic Mucosa	Colon
9	chr19:40866000-40877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:40866400-40872200	Weak transcription	Liver	Liver
11	chr19:40867400-40872000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:40869400-40878800	Weak transcription	HSMM	muscle
13	chr19:40869800-40880200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:40870600-40871800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr19:40870800-40871800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:40870800-40871800	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr19:40871000-40871800	Enhancers	Primary B cells from peripheral blood	blood
18	chr19:40871000-40871800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr19:40871000-40871800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:40871000-40871800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:40871000-40871800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:40871000-40872000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:40871000-40872000	Enhancers	Fetal Heart	heart
24	chr19:40871000-40872200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr19:40871000-40872200	Enhancers	Pancreas	Pancrea
26	chr19:40871000-40872400	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:40871000-40872400	Enhancers	Brain Substantia Nigra	brain
28	chr19:40871000-40872600	Enhancers	Spleen	Spleen
29	chr19:40871000-40872600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr19:40871000-40873400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:40871000-40873600	Weak transcription	Dnd41	blood
32	chr19:40871200-40871800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr19:40871200-40871800	Flanking Active TSS	NHEK	skin
34	chr19:40871200-40872000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr19:40871200-40872000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr19:40871200-40872000	Active TSS	Fetal Intestine Large	intestine
37	chr19:40871200-40872000	Active TSS	Fetal Intestine Small	intestine
38	chr19:40871200-40872000	Active TSS	Hela-S3	cervix
39	chr19:40871200-40872200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:40871200-40872600	Weak transcription	Gastric	stomach
41	chr19:40871200-40872800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr19:40871200-40872800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:40871200-40872800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr19:40871400-40871800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr19:40871400-40871800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr19:40871400-40871800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr19:40871400-40871800	Active TSS	Esophagus	oesophagus
48	chr19:40871400-40871800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr19:40871400-40871800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr19:40871400-40871800	Weak transcription	Small Intestine	intestine

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