Variant report

Variant	rs7249361
Chromosome Location	chr19:52839396-52839397
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	ELF1	chr19:52839165-52839838	SK-N-SH	brain:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
2	CTCF	chr19:52839381-52839461	Kidney_OC	kidney:	n/a	n/a
3	POU2F2	chr19:52839358-52839783	GM12891	blood:	n/a	n/a
4	MYC	chr19:52839378-52839578	H1-hESC	embryonic stem cell:	n/a	n/a
5	NR2C2	chr19:52839329-52839695	HepG2	liver:	n/a	chr19:52839498-52839507 chr19:52839516-52839531
6	SP1	chr19:52839200-52839662	GM12878	blood:	n/a	chr19:52839440-52839452 chr19:52839441-52839450 chr19:52839441-52839455 chr19:52839440-52839452 chr19:52839440-52839451 chr19:52839422-52839432 chr19:52839441-52839450 chr19:52839442-52839451
7	SIN3A	chr19:52839277-52840805	H1-hESC	embryonic stem cell:	n/a	chr19:52839635-52839648
8	GABPA	chr19:52839104-52839983	MCF-7	breast:	n/a	chr19:52839477-52839491 chr19:52839785-52839792 chr19:52839474-52839488
9	POLR2A	chr19:52839213-52839989	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:52839107-52840563	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr19:52839015-52839920	HUVEC	blood vessel:	n/a	n/a
12	PML	chr19:52839102-52839908	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:52839148-52840082	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr19:52839286-52839538	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:52839235-52839834	GM12891	blood:	n/a	n/a
16	GTF2F1	chr19:52839301-52839712	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELF1	chr19:52839232-52839631	HepG2	liver:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
18	ELF1	chr19:52839158-52839826	GM12878	blood:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
19	FOXA1	chr19:52839339-52839823	T-47D	breast:	n/a	n/a
20	ELF1	chr19:52839034-52839882	MCF-7	breast:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
21	ZNF143	chr19:52839350-52839478	H1-hESC	embryonic stem cell:	n/a	n/a
22	HEY1	chr19:52839264-52839663	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:52839266-52839825	H1-hESC	embryonic stem cell:	n/a	n/a
24	EGR1	chr19:52839351-52839603	H1-hESC	embryonic stem cell:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
25	GABPA	chr19:52839250-52839819	HL-60	blood:	n/a	chr19:52839477-52839491 chr19:52839785-52839792 chr19:52839474-52839488
26	EGR1	chr19:52839374-52839590	GM12878	blood:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
27	POLR2A	chr19:52839181-52839718	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:52839216-52839798	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr19:52839294-52839670	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:52839204-52839823	H1-hESC	embryonic stem cell:	n/a	n/a
31	TAF1	chr19:52839199-52839740	GM12878	blood:	n/a	n/a
32	PML	chr19:52839389-52839658	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:52839267-52839698	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr19:52839230-52839791	PBDE	blood:	n/a	n/a
35	POLR2A	chr19:52839269-52839817	GM12878	blood:	n/a	n/a
36	GABPA	chr19:52839354-52839616	HepG2	liver:	n/a	chr19:52839477-52839491 chr19:52839474-52839488
37	POLR2A	chr19:52839175-52839942	GM18951	blood:	n/a	n/a
38	TAF1	chr19:52839162-52839706	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr19:52839178-52841024	IMR90	lung:	n/a	n/a
40	POLR2A	chr19:52839218-52839718	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:52839206-52839707	GM12892	blood:	n/a	n/a
42	EGR1	chr19:52839273-52839739	MCF-7	breast:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
43	NFYB	chr19:52839352-52839583	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:52839139-52840546	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr19:52839254-52839604	HepG2	liver:	n/a	n/a
46	RCOR1	chr19:52839340-52839538	GM12878	blood:	n/a	n/a
47	ELF1	chr19:52839117-52839824	MCF-7	breast:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
48	POLR2A	chr19:52839236-52839745	GM12891	blood:	n/a	n/a
49	TBP	chr19:52839256-52840202	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:52839173-52839769	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
2	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
3	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:
4	chr19:52641710..52644473-chr19:52838292..52841252,2	MCF-7	breast:
5	chr19:52839189..52842101-chr19:52900021..52902093,2	MCF-7	breast:

Variant related genes	Relation type
ZNF610	TF binding region
ENSG00000269102	Chromatin interaction
ENSG00000269834	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000204611	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16983728	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62108271	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6509631	0.92[EUR][1000 genomes]
rs7253555	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
2	chr19:52833000-52839400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:52838600-52839400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:52838600-52839400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr19:52838600-52839400	ZNF genes & repeats	Thymus	Thymus
6	chr19:52838600-52839400	Flanking Active TSS	Dnd41	blood
7	chr19:52838600-52839400	ZNF genes & repeats	NHLF	lung
8	chr19:52838600-52839600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:52838600-52839600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
10	chr19:52838600-52839600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:52838600-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:52838600-52839600	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr19:52838600-52840000	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr19:52838600-52840200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr19:52838600-52840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr19:52838600-52840600	ZNF genes & repeats	Pancreas	Pancrea
17	chr19:52838600-52840600	ZNF genes & repeats	Spleen	Spleen
18	chr19:52838600-52840800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:52838600-52840800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:52838600-52840800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:52838800-52839400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr19:52838800-52839400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr19:52838800-52839400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:52838800-52839400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:52838800-52839400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:52838800-52839400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:52838800-52839400	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:52838800-52839400	ZNF genes & repeats	Fetal Thymus	thymus
29	chr19:52838800-52839400	ZNF genes & repeats	HSMM	muscle
30	chr19:52838800-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:52838800-52839600	Active TSS	Brain Germinal Matrix	brain
32	chr19:52838800-52839800	Active TSS	Primary hematopoietic stem cells	blood
33	chr19:52838800-52840000	Active TSS	Brain Angular Gyrus	brain
34	chr19:52838800-52840000	Active TSS	Brain Anterior Caudate	brain
35	chr19:52838800-52840000	Active TSS	Brain Hippocampus Middle	brain
36	chr19:52838800-52840000	Active TSS	Rectal Smooth Muscle	rectum
37	chr19:52838800-52840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:52838800-52840200	Active TSS	Primary T cells from cord blood	blood
39	chr19:52838800-52840200	Active TSS	Brain Cingulate Gyrus	brain
40	chr19:52838800-52840200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:52838800-52840400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:52838800-52840400	Active TSS	Fetal Brain Female	brain
43	chr19:52838800-52840400	Active TSS	Psoas Muscle	Psoas
44	chr19:52838800-52840400	ZNF genes & repeats	GM12878-XiMat	blood
45	chr19:52838800-52840800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:52838800-52840800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr19:52838800-52841200	Active TSS	Fetal Kidney	kidney
48	chr19:52839000-52839400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr19:52839000-52839400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:52839000-52839400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links