Variant report

Variant	rs6509631
Chromosome Location	chr19:52839474-52839475
allele	C/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	EGR1	chr19:52839406-52839638	GM12878	blood:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
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	MAX	chr19:52839418-52839772	ECC-1	luminal epithelium:	n/a	n/a
13	PML	chr19:52839102-52839908	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:52839148-52840082	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr19:52839286-52839538	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:52839235-52839834	GM12891	blood:	n/a	n/a
17	GTF2F1	chr19:52839301-52839712	H1-hESC	embryonic stem cell:	n/a	n/a
18	ELF1	chr19:52839232-52839631	HepG2	liver:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
19	ELF1	chr19:52839158-52839826	GM12878	blood:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
20	FOXA1	chr19:52839339-52839823	T-47D	breast:	n/a	n/a
21	ELF1	chr19:52839034-52839882	MCF-7	breast:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
22	ZNF143	chr19:52839350-52839478	H1-hESC	embryonic stem cell:	n/a	n/a
23	HEY1	chr19:52839264-52839663	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:52839266-52839825	H1-hESC	embryonic stem cell:	n/a	n/a
25	EGR1	chr19:52839351-52839603	H1-hESC	embryonic stem cell:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
26	GABPA	chr19:52839250-52839819	HL-60	blood:	n/a	chr19:52839477-52839491 chr19:52839785-52839792 chr19:52839474-52839488
27	EGR1	chr19:52839374-52839590	GM12878	blood:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
28	POLR2A	chr19:52839181-52839718	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:52839216-52839798	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr19:52839294-52839670	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr19:52839204-52839823	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr19:52839199-52839740	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr19:52839429-52839610	HepG2	liver:	n/a	n/a
34	PML	chr19:52839389-52839658	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:52839267-52839698	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr19:52839230-52839791	PBDE	blood:	n/a	n/a
37	MXI1	chr19:52839407-52839631	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr19:52839269-52839817	GM12878	blood:	n/a	n/a
39	GABPA	chr19:52839354-52839616	HepG2	liver:	n/a	chr19:52839477-52839491 chr19:52839474-52839488
40	POLR2A	chr19:52839175-52839942	GM18951	blood:	n/a	n/a
41	TAF1	chr19:52839162-52839706	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr19:52839178-52841024	IMR90	lung:	n/a	n/a
43	POLR2A	chr19:52839218-52839718	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:52839206-52839707	GM12892	blood:	n/a	n/a
45	EGR1	chr19:52839273-52839739	MCF-7	breast:	n/a	chr19:52839513-52839527 chr19:52839478-52839487
46	NFYB	chr19:52839352-52839583	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:52839139-52840546	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr19:52839254-52839604	HepG2	liver:	n/a	n/a
49	RCOR1	chr19:52839340-52839538	GM12878	blood:	n/a	n/a
50	MYC	chr19:52839442-52839600	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52839445-52839495	PrEC	prostate:	n/a
2	chr19:52839445-52839495	U87	brain:	n/a
3	chr19:52839445-52839495	NHDF-neo	bronchial:	n/a
4	chr19:52839445-52839495	NHBE	bronchial:	n/a
5	chr19:52839445-52839495	ProgFib	skin:	n/a
6	chr19:52839445-52839495	BJ	skin:	n/a
7	chr19:52839445-52839495	SAEC	small airway:	n/a
8	chr19:52839445-52839495	ovcar-3	ovarian:	n/a
9	chr19:52839445-52839495	K562	blood:	n/a
10	chr19:52839445-52839495	A549	lung:	n/a
11	chr19:52839445-52839495	LNCaP	prostate:	n/a
12	chr19:52839445-52839495	HRE	kidney:	n/a
13	chr19:52839445-52839495	GM12878	blood:	n/a
14	chr19:52839445-52839495	HIPEpiC	eye:	n/a
15	chr19:52839445-52839495	PFSK-1	brain:	n/a
16	chr19:52839445-52839495	HL-60	blood:	n/a
17	chr19:52839445-52839495	HRCEpiC	kidney:	n/a
18	chr19:52839445-52839495	Hepatocyte	liver:	n/a
19	chr19:52839445-52839495	MCF10A-Er-Src	breast:	n/a
20	chr19:52839445-52839495	Caco-2	colon:	n/a
21	chr19:52839445-52839495	HCT-116	colon:	n/a
22	chr19:52839445-52839495	HCF	heart:	n/a
23	chr19:52839445-52839495	GM06990	blood:	n/a
24	chr19:52839445-52839495	HMEC	breast:	n/a
25	chr19:52839445-52839495	HCPEpiC	choroid plexus:	n/a
26	chr19:52839445-52839495	AG04450	lung:	fetal
27	chr19:52839445-52839495	HepG2	liver:	n/a
28	chr19:52839445-52839495	NH-A	brain:	n/a
29	chr19:52839445-52839495	AoSMC	blood vessel:	n/a
30	chr19:52839445-52839495	T-47D	breast:	n/a
31	chr19:52839445-52839495	PANC-1	pancreas:	n/a
32	chr19:52839445-52839495	AG04449	skin:	fetal
33	chr19:52839445-52839495	NT2-D1	testis:	n/a
34	chr19:52839445-52839495	SK-N-SH_RA	brain:	n/a
35	chr19:52839445-52839495	IMR90	lung:	fetal
36	chr19:52839445-52839495	SK-N-MC	brain:	n/a
37	chr19:52839445-52839495	SK-N-SH	brain:	n/a
38	chr19:52839445-52839495	AG09309	skin:	n/a
39	chr19:52839445-52839495	HNPCEpiC	eye:	n/a
40	chr19:52839445-52839495	SKMC	muscle:	n/a
41	chr19:52839445-52839495	CMK	blood:	n/a
42	chr19:52839445-52839495	HEEpiC	esophagus:	n/a
43	chr19:52839445-52839495	HPAEpiC	pulmonary alveolar:	n/a
44	chr19:52839445-52839495	ECC-1	luminal epithelium:	n/a
45	chr19:52839445-52839495	GM12891	blood:	n/a
46	chr19:52839445-52839495	HCM	heart:	n/a
47	chr19:52839445-52839495	HEK293	kidney:	embryo
48	chr19:52839445-52839495	AG10803	skin:	n/a
49	chr19:52839445-52839495	GM19239	blood:	n/a
50	chr19:52839445-52839495	Jurkat	blood:	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
ZNF610	CpG island
ENSG00000198464	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000269834	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10416012	1.00[CEU][hapmap]
rs11880474	0.85[CEU][hapmap]
rs16983718	0.85[CEU][hapmap]
rs16983728	0.92[EUR][1000 genomes]
rs2560903	0.85[CEU][hapmap]
rs2657932	0.85[CEU][hapmap]
rs321908	0.85[CEU][hapmap]
rs321921	0.87[YRI][hapmap]
rs321927	1.00[CEU][hapmap]
rs62108271	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7249361	0.92[EUR][1000 genomes]
rs7253555	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8103072	0.82[CEU][hapmap]

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:123 , 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	chr19:52838600-52839600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:52838600-52839600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
4	chr19:52838600-52839600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:52838600-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:52838600-52839600	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:52838600-52840000	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr19:52838600-52840200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr19:52838600-52840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr19:52838600-52840600	ZNF genes & repeats	Pancreas	Pancrea
11	chr19:52838600-52840600	ZNF genes & repeats	Spleen	Spleen
12	chr19:52838600-52840800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:52838600-52840800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:52838600-52840800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:52838800-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:52838800-52839600	Active TSS	Brain Germinal Matrix	brain
17	chr19:52838800-52839800	Active TSS	Primary hematopoietic stem cells	blood
18	chr19:52838800-52840000	Active TSS	Brain Angular Gyrus	brain
19	chr19:52838800-52840000	Active TSS	Brain Anterior Caudate	brain
20	chr19:52838800-52840000	Active TSS	Brain Hippocampus Middle	brain
21	chr19:52838800-52840000	Active TSS	Rectal Smooth Muscle	rectum
22	chr19:52838800-52840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:52838800-52840200	Active TSS	Primary T cells from cord blood	blood
24	chr19:52838800-52840200	Active TSS	Brain Cingulate Gyrus	brain
25	chr19:52838800-52840200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:52838800-52840400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:52838800-52840400	Active TSS	Fetal Brain Female	brain
28	chr19:52838800-52840400	Active TSS	Psoas Muscle	Psoas
29	chr19:52838800-52840400	ZNF genes & repeats	GM12878-XiMat	blood
30	chr19:52838800-52840800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:52838800-52840800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr19:52838800-52841200	Active TSS	Fetal Kidney	kidney
33	chr19:52839000-52839600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr19:52839000-52839600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr19:52839000-52839600	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:52839000-52839800	Active TSS	Primary B cells from cord blood	blood
37	chr19:52839000-52839800	Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr19:52839000-52839800	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr19:52839000-52840000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:52839000-52840000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr19:52839000-52840200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:52839000-52840200	Active TSS	Brain Substantia Nigra	brain
43	chr19:52839000-52840200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr19:52839000-52840200	Active TSS	Fetal Stomach	stomach
45	chr19:52839000-52840200	Active TSS	Left Ventricle	heart
46	chr19:52839000-52840200	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr19:52839000-52840400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:52839000-52840400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:52839000-52840400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:52839000-52840400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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