Variant report

Variant	rs1919471
Chromosome Location	chr4:74486245-74486246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:105)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:105 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr4:74486185-74486525	ECC-1	luminal epithelium:	n/a	chr4:74486358-74486370 chr4:74486356-74486371
2	MAX	chr4:74485928-74486605	A549	lung:	n/a	n/a
3	CTCF	chr4:74486016-74486282	GM12878	blood:	n/a	n/a
4	MAX	chr4:74485897-74486662	A549	lung:	n/a	n/a
5	EP300	chr4:74485790-74486565	GM12878	blood:	n/a	chr4:74486327-74486340 chr4:74486361-74486371 chr4:74485890-74485897
6	UBTF	chr4:74486078-74486304	K562	blood:	n/a	n/a
7	POLR2A	chr4:74486197-74486457	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr4:74486108-74486249	GM12891	blood:	n/a	n/a
9	POLR2A	chr4:74484623-74486579	GM19099	blood:	n/a	n/a
10	POLR2A	chr4:74486001-74486436	GM12878	blood:	n/a	n/a
11	CTCF	chr4:74486100-74486250	HMEC	breast:	n/a	n/a
12	MAX	chr4:74485989-74486435	H1-hESC	embryonic stem cell:	n/a	n/a
13	EBF1	chr4:74486056-74486424	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:74485975-74486509	HCT-116	colon:	n/a	n/a
15	ZEB1	chr4:74485814-74486423	HepG2	liver:	n/a	n/a
16	CTCF	chr4:74486089-74486277	HepG2	liver:	n/a	n/a
17	CTCF	chr4:74486100-74486250	HRE	kidney:	n/a	n/a
18	ZNF384	chr4:74486229-74486429	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:74485916-74486508	GM12878	blood:	n/a	n/a
20	PBX3	chr4:74486192-74486449	A549	lung:	n/a	n/a
21	HMGN3	chr4:74486052-74486375	K562	blood:	n/a	n/a
22	TCF12	chr4:74485828-74486573	A549	lung:	n/a	n/a
23	NRF1	chr4:74486088-74486329	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr4:74485986-74486437	K562	blood:	n/a	n/a
25	POLR2A	chr4:74485881-74486500	GM19193	blood:	n/a	n/a
26	POLR2A	chr4:74486153-74486272	A549	lung:	n/a	n/a
27	POU2F2	chr4:74485980-74486535	GM12878	blood:	n/a	n/a
28	MAZ	chr4:74486194-74486326	HepG2	liver:	n/a	n/a
29	SPI1	chr4:74486176-74486532	HL-60	blood:	n/a	n/a
30	SIN3AK20	chr4:74485814-74486587	HCT-116	colon:	n/a	n/a
31	RAD21	chr4:74486024-74486350	H1-hESC	embryonic stem cell:	n/a	n/a
32	BACH1	chr4:74486147-74486407	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr4:74486111-74486548	GM12878	blood:	n/a	n/a
34	SETDB1	chr4:74485901-74486606	U2OS	brain:	n/a	n/a
35	RFX5	chr4:74485946-74486408	GM12878	blood:	n/a	n/a
36	MAX	chr4:74486121-74486520	Hela-S3	cervix:	n/a	n/a
37	SIN3AK20	chr4:74486152-74486485	A549	lung:	n/a	n/a
38	SP1	chr4:74486093-74486598	A549	lung:	n/a	n/a
39	RAD21	chr4:74485870-74486548	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr4:74486064-74486275	GM19238	blood:	n/a	n/a
41	WRNIP1	chr4:74485945-74486532	GM12878	blood:	n/a	n/a
42	SPI1	chr4:74486206-74486391	K562	blood:	n/a	n/a
43	FOXA1	chr4:74486138-74486507	T-47D	breast:	n/a	chr4:74486358-74486370 chr4:74486356-74486371
44	CTCF	chr4:74486140-74486290	K562	blood:	n/a	n/a
45	FOS	chr4:74485843-74486435	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr4:74486243-74486433	MCF10A-Er-Src	breast:	n/a	n/a
47	RAD21	chr4:74486022-74486291	HepG2	liver:	n/a	n/a
48	RCOR1	chr4:74486066-74486452	K562	blood:	n/a	n/a
49	MAX	chr4:74485833-74486545	ECC-1	luminal epithelium:	n/a	n/a
50	USF1	chr4:74485993-74486572	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:74486230-74486280	CMK	blood:	n/a
2	chr4:74486230-74486280	HPAEpiC	pulmonary alveolar:	n/a
3	chr4:74486230-74486280	U87	brain:	n/a
4	chr4:74486230-74486280	PrEC	prostate:	n/a
5	chr4:74486230-74486280	T-47D	breast:	n/a
6	chr4:74486230-74486280	ECC-1	luminal epithelium:	n/a
7	chr4:74486230-74486280	AG09319	gingival:	n/a
8	chr4:74486230-74486280	NHBE	bronchial:	n/a
9	chr4:74486230-74486280	AG09309	skin:	n/a
10	chr4:74486230-74486280	HRCEpiC	kidney:	n/a
11	chr4:74486230-74486280	HRE	kidney:	n/a
12	chr4:74486230-74486280	HUVEC	blood vessel:	n/a
13	chr4:74486230-74486280	Jurkat	blood:	n/a
14	chr4:74486230-74486280	Hela-S3	cervix:	n/a
15	chr4:74486230-74486280	SK-N-MC	brain:	n/a
16	chr4:74486230-74486280	SK-N-SH_RA	brain:	n/a
17	chr4:74486230-74486280	Caco-2	colon:	n/a
18	chr4:74486230-74486280	HRPEpiC	eye:	n/a
19	chr4:74486230-74486280	NB4	blood:	n/a
20	chr4:74486230-74486280	PANC-1	pancreas:	n/a
21	chr4:74486230-74486280	NHDF-neo	bronchial:	n/a
22	chr4:74486230-74486280	MCF-7	breast:	n/a
23	chr4:74486230-74486280	BJ	skin:	n/a
24	chr4:74486230-74486280	NT2-D1	testis:	n/a
25	chr4:74486230-74486280	Hepatocyte	liver:	n/a
26	chr4:74486230-74486280	NH-A	brain:	n/a
27	chr4:74486230-74486280	GM12878	blood:	n/a
28	chr4:74486230-74486280	SK-N-SH	brain:	n/a
29	chr4:74486230-74486280	SAEC	small airway:	n/a
30	chr4:74486230-74486280	GM12892	blood:	n/a
31	chr4:74486230-74486280	AG04450	lung:	fetal
32	chr4:74486230-74486280	HCT-116	colon:	n/a
33	chr4:74486230-74486280	HEEpiC	esophagus:	n/a
34	chr4:74486230-74486280	MCF10A-Er-Src	breast:	n/a
35	chr4:74486230-74486280	K562	blood:	n/a
36	chr4:74486230-74486280	HNPCEpiC	eye:	n/a
37	chr4:74486230-74486280	GM06990	blood:	n/a
38	chr4:74486230-74486280	HCPEpiC	choroid plexus:	n/a
39	chr4:74486230-74486280	HIPEpiC	eye:	n/a
40	chr4:74486230-74486280	A549	lung:	n/a
41	chr4:74486230-74486280	HMEC	breast:	n/a
42	chr4:74486230-74486280	PFSK-1	brain:	n/a
43	chr4:74486230-74486280	AG04449	skin:	fetal
44	chr4:74486230-74486280	AoSMC	blood vessel:	n/a
45	chr4:74486230-74486280	HepG2	liver:	n/a
46	chr4:74486230-74486280	IMR90	lung:	fetal
47	chr4:74486230-74486280	ProgFib	skin:	n/a
48	chr4:74486230-74486280	HCM	heart:	n/a
49	chr4:74486230-74486280	BE2_C	brain:	n/a
50	chr4:74486230-74486280	HCF	heart:	n/a

No data

Variant related genes	Relation type
RASSF6	TF binding region
RASSF6	CpG island

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10003721	0.84[CEU][hapmap];0.96[GIH][hapmap]
rs1247669	0.85[CEU][hapmap]
rs16849717	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17838981	0.96[GIH][hapmap]
rs2272427	0.96[GIH][hapmap]
rs3756068	0.84[CEU][hapmap];0.96[GIH][hapmap]
rs72863058	0.95[EUR][1000 genomes]
rs7658159	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1919471	RASSF6	Cis_1M	lymphoblastoid	RTeQTL
rs1919471	C4orf7	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74482000-74487000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:74484400-74486400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:74484400-74486400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:74484400-74486400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr4:74484400-74486800	Active TSS	Fetal Stomach	stomach
6	chr4:74484600-74486600	Active TSS	Fetal Intestine Large	intestine
7	chr4:74484800-74486600	Active TSS	Duodenum Mucosa	Duodenum
8	chr4:74484800-74486600	Active TSS	Fetal Intestine Small	intestine
9	chr4:74485000-74486600	Active TSS	Colonic Mucosa	Colon
10	chr4:74485000-74486800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:74485000-74486800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:74485200-74486800	Active TSS	Fetal Kidney	kidney
13	chr4:74485400-74486600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:74485400-74486600	Flanking Active TSS	Fetal Thymus	thymus
15	chr4:74485400-74486800	Active TSS	Thymus	Thymus
16	chr4:74485600-74486400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:74485600-74486400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:74485600-74486400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:74485600-74486600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:74485600-74486600	Active TSS	Esophagus	oesophagus
21	chr4:74485600-74486800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:74485800-74486400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:74485800-74486400	Active TSS	Primary B cells from cord blood	blood
24	chr4:74485800-74486400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:74485800-74486400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:74485800-74486400	Bivalent/Poised TSS	Fetal Lung	lung
27	chr4:74485800-74486400	Active TSS	Lung	lung
28	chr4:74485800-74486400	Active TSS	Ovary	ovary
29	chr4:74485800-74486400	Bivalent/Poised TSS	Small Intestine	intestine
30	chr4:74485800-74486400	Active TSS	HMEC	breast
31	chr4:74485800-74486400	Active TSS	K562	blood
32	chr4:74485800-74486400	Bivalent/Poised TSS	Osteobl	bone
33	chr4:74485800-74486600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr4:74485800-74486600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr4:74485800-74486600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:74485800-74486600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:74485800-74486600	Active TSS	Placenta	Placenta
38	chr4:74485800-74486800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr4:74485800-74486800	Active TSS	Hela-S3	cervix
40	chr4:74485800-74490600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:74486000-74486400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:74486000-74486400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:74486000-74486400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:74486000-74486400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:74486000-74486400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr4:74486000-74486400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:74486000-74486400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:74486000-74486400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:74486000-74486400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
50	chr4:74486000-74486400	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood

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