Variant report

Variant	rs4632259
Chromosome Location	chr19:38924362-38924363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:65)
CpG islands
(count:244)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:65 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr19:38924127-38924551	K562	blood:	n/a	chr19:38924283-38924292 chr19:38924386-38924395
2	MAX	chr19:38923876-38924509	K562	blood:	n/a	chr19:38924418-38924428
3	CTCF	chr19:38924286-38924369	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr19:38924138-38924406	SK-N-SH	brain:	n/a	n/a
5	MYC	chr19:38923969-38924417	K562	blood:	n/a	n/a
6	TAF7	chr19:38923967-38924469	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr19:38924101-38924370	K562	blood:	n/a	n/a
8	ZBTB7A	chr19:38924056-38924641	K562	blood:	n/a	n/a
9	REST	chr19:38924116-38924472	SK-N-SH	brain:	n/a	n/a
10	REST	chr19:38924124-38924386	K562	blood:	n/a	n/a
11	POLR2A	chr19:38924025-38924409	K562	blood:	n/a	n/a
12	EGR1	chr19:38924140-38924373	K562	blood:	n/a	chr19:38924278-38924291
13	REST	chr19:38924036-38924524	HCT-116	colon:	n/a	n/a
14	IRF1	chr19:38924047-38924391	K562	blood:	n/a	chr19:38924282-38924296
15	SPI1	chr19:38924035-38924377	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:38924044-38924608	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr19:38924187-38924366	GM12878	blood:	n/a	n/a
18	TBP	chr19:38923975-38924410	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr19:38924003-38924374	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr19:38924082-38924384	U87	brain:	n/a	n/a
21	MAX	chr19:38924129-38924362	K562	blood:	n/a	n/a
22	REST	chr19:38924139-38924365	SK-N-SH	brain:	n/a	n/a
23	REST	chr19:38924078-38924392	GM12878	blood:	n/a	n/a
24	REST	chr19:38924116-38924411	HCT-116	colon:	n/a	n/a
25	HEY1	chr19:38923965-38924391	K562	blood:	n/a	n/a
26	REST	chr19:38924017-38924568	K562	blood:	n/a	n/a
27	TBP	chr19:38924091-38924410	K562	blood:	n/a	n/a
28	YY1	chr19:38923990-38924385	K562	blood:	n/a	chr19:38924283-38924292
29	REST	chr19:38923943-38924363	A549	lung:	n/a	n/a
30	SIN3AK20	chr19:38924069-38924376	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr19:38923990-38924370	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP1	chr19:38923976-38924389	H1-hESC	embryonic stem cell:	n/a	chr19:38924284-38924293 chr19:38924283-38924292 chr19:38924284-38924293 chr19:38924282-38924294 chr19:38924171-38924182 chr19:38924282-38924294
33	MAX	chr19:38923908-38924545	H1-hESC	embryonic stem cell:	n/a	chr19:38924418-38924428
34	POLR2A	chr19:38923987-38924491	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr19:38924058-38924551	ECC-1	luminal epithelium:	n/a	chr19:38924418-38924428
36	REST	chr19:38923996-38924536	ECC-1	luminal epithelium:	n/a	n/a
37	REST	chr19:38924168-38924372	GM12878	blood:	n/a	n/a
38	REST	chr19:38924176-38924404	PANC-1	pancreas:	n/a	n/a
39	ELF1	chr19:38923902-38924415	K562	blood:	n/a	n/a
40	NFYB	chr19:38924131-38924429	GM12878	blood:	n/a	n/a
41	RCOR1	chr19:38923929-38924600	K562	blood:	n/a	n/a
42	MAZ	chr19:38923966-38924530	K562	blood:	n/a	chr19:38924418-38924428
43	ZNF143	chr19:38923943-38924683	H1-hESC	embryonic stem cell:	n/a	n/a
44	EGR1	chr19:38924134-38924375	K562	blood:	n/a	chr19:38924278-38924291
45	POLR2A	chr19:38923812-38926008	H1-hESC	embryonic stem cell:	n/a	n/a
46	CBX3	chr19:38923925-38924364	K562	blood:	n/a	n/a
47	REST	chr19:38923935-38924411	A549	lung:	n/a	n/a
48	NFYB	chr19:38924103-38924472	K562	blood:	n/a	n/a
49	MAX	chr19:38924155-38924466	K562	blood:	n/a	chr19:38924418-38924428
50	REST	chr19:38924103-38924408	HL-60	blood:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38924347-38924397	Caco-2	colon:	n/a
2	chr19:38924349-38924399	NH-A	brain:	n/a
3	chr19:38924349-38924399	HL-60	blood:	n/a
4	chr19:38924319-38924369	AoSMC	blood vessel:	n/a
5	chr19:38924330-38924380	AG10803	skin:	n/a
6	chr19:38924330-38924380	NT2-D1	testis:	n/a
7	chr19:38924347-38924397	GM12891	blood:	n/a
8	chr19:38924319-38924369	T-47D	breast:	n/a
9	chr19:38924349-38924399	U87	brain:	n/a
10	chr19:38924319-38924369	HRPEpiC	eye:	n/a
11	chr19:38924319-38924369	NT2-D1	testis:	n/a
12	chr19:38924330-38924380	SK-N-SH	brain:	n/a
13	chr19:38924330-38924380	SK-N-MC	brain:	n/a
14	chr19:38924347-38924397	HL-60	blood:	n/a
15	chr19:38924347-38924397	T-47D	breast:	n/a
16	chr19:38924349-38924399	ECC-1	luminal epithelium:	n/a
17	chr19:38924349-38924399	SAEC	small airway:	n/a
18	chr19:38924349-38924399	HEK293	kidney:	embryo
19	chr19:38924347-38924397	LNCaP	prostate:	n/a
20	chr19:38924349-38924399	HCT-116	colon:	n/a
21	chr19:38924349-38924399	AG10803	skin:	n/a
22	chr19:38924349-38924399	HCM	heart:	n/a
23	chr19:38924319-38924369	HMEC	breast:	n/a
24	chr19:38924349-38924399	ovcar-3	ovarian:	n/a
25	chr19:38924319-38924369	H1-hESC	embryonic stem cell:	embryo
26	chr19:38924349-38924399	HRCEpiC	kidney:	n/a
27	chr19:38924330-38924380	T-47D	breast:	n/a
28	chr19:38924347-38924397	ovcar-3	ovarian:	n/a
29	chr19:38924330-38924380	GM12891	blood:	n/a
30	chr19:38924347-38924397	PrEC	prostate:	n/a
31	chr19:38924347-38924397	Jurkat	blood:	n/a
32	chr19:38924319-38924369	NHBE	bronchial:	n/a
33	chr19:38924349-38924399	SK-N-SH	brain:	n/a
34	chr19:38924349-38924399	Hepatocyte	liver:	n/a
35	chr19:38924347-38924397	RPTEC	kidney:	n/a
36	chr19:38924347-38924397	AG10803	skin:	n/a
37	chr19:38924347-38924397	MCF10A-Er-Src	breast:	n/a
38	chr19:38924349-38924399	Caco-2	colon:	n/a
39	chr19:38924347-38924397	HCPEpiC	choroid plexus:	n/a
40	chr19:38924330-38924380	MCF-7	breast:	n/a
41	chr19:38924330-38924380	GM12878	blood:	n/a
42	chr19:38924349-38924399	HRE	kidney:	n/a
43	chr19:38924319-38924369	SKMC	muscle:	n/a
44	chr19:38924347-38924397	NHBE	bronchial:	n/a
45	chr19:38924347-38924397	SAEC	small airway:	n/a
46	chr19:38924330-38924380	HRCEpiC	kidney:	n/a
47	chr19:38924330-38924380	HepG2	liver:	n/a
48	chr19:38924347-38924397	HCF	heart:	n/a
49	chr19:38924330-38924380	Jurkat	blood:	n/a
50	chr19:38924330-38924380	MCF10A-Er-Src	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38879240..38881217-chr19:38924202..38926113,2	MCF-7	breast:

No data

Variant related genes	Relation type
RYR1	TF binding region
RYR1	CpG island
ENSG00000188766	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11880126	1.00[CHD][hapmap]
rs16972591	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61328448	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7248350	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1055309	chr19:38896244-38945851	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1065803	chr19:38903099-38945851	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1066138	chr19:38904072-38949729	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38920400-38924800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:38920600-38924400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:38920600-38924600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:38922200-38924400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:38923800-38924600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:38923800-38924600	Bivalent Enhancer	Placenta	Placenta
7	chr19:38923800-38925000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:38923800-38926000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:38923800-38926200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:38924000-38924400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:38924000-38924400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
12	chr19:38924000-38924400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr19:38924000-38924400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:38924000-38924400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:38924000-38924400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:38924000-38924400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:38924000-38924400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:38924000-38924400	Enhancers	Spleen	Spleen
19	chr19:38924000-38924600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:38924000-38924600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:38924000-38924600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:38924000-38924600	Enhancers	Gastric	stomach
23	chr19:38924000-38924600	ZNF genes & repeats	Right Atrium	heart
24	chr19:38924000-38924600	Enhancers	GM12878-XiMat	blood
25	chr19:38924000-38924600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr19:38924000-38924800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38924000-38924800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:38924000-38924800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr19:38924000-38924800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:38924000-38924800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:38924000-38925000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:38924000-38925000	Active TSS	HSMM	muscle
33	chr19:38924000-38925200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:38924000-38925200	Active TSS	Psoas Muscle	Psoas
35	chr19:38924000-38925400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
36	chr19:38924000-38925400	Bivalent Enhancer	A549	lung
37	chr19:38924000-38925600	Active TSS	H9 Cell Line	embryonic stem cell
38	chr19:38924000-38925600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:38924000-38925600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr19:38924000-38925800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
41	chr19:38924000-38926400	Active TSS	HSMMtube	muscle
42	chr19:38924200-38924400	Active TSS	Fetal Muscle Leg	muscle
43	chr19:38924200-38924600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr19:38924200-38924600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:38924200-38924600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
46	chr19:38924200-38924600	Active TSS	K562	blood
47	chr19:38924200-38924800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr19:38924200-38925000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
49	chr19:38924200-38925600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:38924200-38925600	Active TSS	Skeletal Muscle Female	skeletal muscle

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