Variant report

Variant	rs11731505
Chromosome Location	chr4:85503575-85503576
allele	A/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	MAZ	chr4:85503255-85504622	IMR90	lung:	n/a	chr4:85503952-85503962
2	RCOR1	chr4:85503335-85504348	K562	blood:	n/a	n/a
3	SP4	chr4:85503425-85504160	H1-hESC	embryonic stem cell:	n/a	chr4:85503952-85503968 chr4:85503865-85503881 chr4:85504029-85504045 chr4:85504031-85504047 chr4:85503954-85503970
4	YY1	chr4:85503399-85503941	ECC-1	luminal epithelium:	n/a	chr4:85503872-85503881 chr4:85503855-85503869 chr4:85503858-85503872
5	MAX	chr4:85503574-85504583	HepG2	liver:	n/a	chr4:85503952-85503962
6	MAX	chr4:85503288-85505307	ECC-1	luminal epithelium:	n/a	chr4:85503952-85503962
7	MAX	chr4:85503415-85505025	HepG2	liver:	n/a	chr4:85503952-85503962
8	NFIC	chr4:85503270-85504020	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr4:85503476-85504175	MCF-7	breast:	n/a	chr4:85503952-85503962
10	EGR1	chr4:85503495-85504216	MCF-7	breast:	n/a	chr4:85503868-85503878 chr4:85503952-85503965 chr4:85503952-85503966 chr4:85503955-85503964 chr4:85503953-85503967 chr4:85503952-85503965 chr4:85503951-85503966 chr4:85503870-85503883 chr4:85503907-85503921 chr4:85503955-85503965 chr4:85503952-85503965 chr4:85503953-85503964 chr4:85503952-85503965 chr4:85503999-85504009 chr4:85503871-85503882
11	TCF7L2	chr4:85503502-85503922	MCF-7	breast:	n/a	n/a
12	GTF2F1	chr4:85503372-85503968	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:85503345-85504108	MCF-7	breast:	n/a	chr4:85503952-85503962
14	TCF12	chr4:85503324-85504408	ECC-1	luminal epithelium:	n/a	n/a
15	CREB1	chr4:85503529-85504260	HepG2	liver:	n/a	chr4:85503980-85503993
16	SP1	chr4:85503141-85504958	HCT-116	colon:	n/a	chr4:85503998-85504010 chr4:85504718-85504732 chr4:85503869-85503878 chr4:85504035-85504044 chr4:85504205-85504214 chr4:85504033-85504045 chr4:85504000-85504009 chr4:85503958-85503967 chr4:85504034-85504044 chr4:85503868-85503877 chr4:85504204-85504216 chr4:85503995-85504009 chr4:85504030-85504044 chr4:85504216-85504230 chr4:85504033-85504045 chr4:85503999-85504008 chr4:85504035-85504044 chr4:85503956-85503968 chr4:85503957-85503967 chr4:85503867-85503879 chr4:85503998-85504010 chr4:85504205-85504214 chr4:85503890-85503904 chr4:85503957-85503967 chr4:85504034-85504043 chr4:85503958-85503967 chr4:85504083-85504096 chr4:85503956-85503968 chr4:85504034-85504044 chr4:85503867-85503879 chr4:85503957-85503966 chr4:85504206-85504215 chr4:85503874-85503888
17	MAX	chr4:85503516-85504472	H1-hESC	embryonic stem cell:	n/a	chr4:85503952-85503962
18	YY1	chr4:85503447-85503741	HCT-116	colon:	n/a	n/a
19	TCF12	chr4:85503266-85504434	MCF-7	breast:	n/a	n/a
20	NR2F2	chr4:85503235-85504048	MCF-7	breast:	n/a	chr4:85503506-85503521
21	TBP	chr4:85503430-85504405	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr4:85503406-85503940	ECC-1	luminal epithelium:	n/a	chr4:85503872-85503881 chr4:85503855-85503869 chr4:85503858-85503872
23	TEAD4	chr4:85503428-85503894	MCF-7	breast:	n/a	n/a
24	ESR1	chr4:85503480-85503803	T-47D	breast:	n/a	n/a
25	TCF7L2	chr4:85503421-85505179	HCT-116	colon:	n/a	n/a
26	KAP1	chr4:85503332-85503841	HEK293	kidney:	n/a	n/a
27	CHD2	chr4:85503408-85504825	H1-hESC	embryonic stem cell:	n/a	chr4:85504204-85504214 chr4:85503897-85503907 chr4:85504287-85504297
28	GATA3	chr4:85503289-85504114	MCF-7	breast:	n/a	n/a
29	JUND	chr4:85503510-85503758	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr4:85503333-85503869	T-47D	breast:	n/a	n/a
31	POLR2A	chr4:85503543-85505328	H1-neurons	neurons:	n/a	n/a
32	REST	chr4:85503380-85505244	H1-neurons	neurons:	n/a	chr4:85503763-85503770
33	TEAD4	chr4:85503309-85504105	HCT-116	colon:	n/a	n/a
34	TAF7	chr4:85503335-85503972	H1-hESC	embryonic stem cell:	n/a	n/a
35	CREB1	chr4:85503476-85504214	ECC-1	luminal epithelium:	n/a	chr4:85503980-85503993
36	MAX	chr4:85503242-85505335	HCT-116	colon:	n/a	chr4:85503952-85503962
37	CTCF	chr4:85503520-85503670	Caco-2	colon:	n/a	n/a
38	POLR2A	chr4:85503419-85504910	ECC-1	luminal epithelium:	n/a	n/a
39	ESR1	chr4:85503427-85503865	T-47D	breast:	n/a	n/a
40	POLR2A	chr4:85503268-85505172	H1-hESC	embryonic stem cell:	n/a	n/a
41	EGR1	chr4:85503481-85504141	ECC-1	luminal epithelium:	n/a	chr4:85503868-85503878 chr4:85503952-85503965 chr4:85503952-85503966 chr4:85503955-85503964 chr4:85503953-85503967 chr4:85503952-85503965 chr4:85503951-85503966 chr4:85503870-85503883 chr4:85503907-85503921 chr4:85503955-85503965 chr4:85503952-85503965 chr4:85503953-85503964 chr4:85503952-85503965 chr4:85503999-85504009 chr4:85503871-85503882
42	YY1	chr4:85503529-85503727	HCT-116	colon:	n/a	n/a
43	TEAD4	chr4:85503347-85503889	MCF-7	breast:	n/a	n/a
44	EP300	chr4:85503375-85503889	T-47D	breast:	n/a	n/a
45	NANOG	chr4:85503540-85504212	H1-hESC	embryonic stem cell:	n/a	n/a
46	EP300	chr4:85503359-85504030	ECC-1	luminal epithelium:	n/a	chr4:85503943-85503959
47	POLR2A	chr4:85503346-85503995	H1-hESC	embryonic stem cell:	n/a	n/a
48	CHD1	chr4:85503413-85503789	H1-hESC	embryonic stem cell:	n/a	n/a
49	ZNF217	chr4:85503370-85503864	MCF-7	breast:	n/a	n/a
50	ATF2	chr4:85503453-85504139	H1-hESC	embryonic stem cell:	n/a	chr4:85503979-85503993 chr4:85503981-85503992

No.	Distal block	Cell Line	Cell type
1	chr4:85503502..85505436-chr4:85887662..85889953,2	MCF-7	breast:
2	chr4:85503339..85505737-chr4:85885750..85887907,3	MCF-7	breast:
3	chr4:85502738..85504984-chr4:89443554..89446248,2	MCF-7	breast:
4	chr4:85502040..85503773-chr4:85544764..85547239,2	MCF-7	breast:
5	chr4:85483371..85486524-chr4:85499401..85503831,3	MCF-7	breast:
6	chr4:85502095..85504944-chr4:85602108..85604379,3	MCF-7	breast:

Variant related genes	Relation type
CDS1	TF binding region
ENSG00000138641	Chromatin interaction
ENSG00000180769	Chromatin interaction
ENSG00000145337	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10516725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725803	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737002	1.00[AMR][1000 genomes]
rs11939816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944727	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944769	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17367317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17367775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17368157	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17375734	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376293	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17376461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs17376946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs36068434	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41524654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73831542	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699828	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3427170	chr4:85503153-85505701	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85503000-85503600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
2	chr4:85503000-85503600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
3	chr4:85503000-85503600	Flanking Active TSS	Fetal Heart	heart
4	chr4:85503000-85503800	Flanking Active TSS	HMEC	breast
5	chr4:85503200-85503600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
6	chr4:85503200-85503600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:85503200-85503600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:85503200-85503600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
9	chr4:85503200-85503600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:85503200-85503600	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr4:85503200-85503600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
12	chr4:85503200-85503800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:85503200-85503800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr4:85503200-85503800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:85503200-85503800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr4:85503200-85503800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:85503200-85503800	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr4:85503200-85503800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr4:85503200-85503800	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr4:85503200-85503800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr4:85503200-85503800	Flanking Active TSS	NHEK	skin
22	chr4:85503200-85504000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:85503200-85505000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:85503200-85505000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:85503200-85505400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr4:85503200-85505600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr4:85503400-85503600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:85503400-85503600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:85503400-85503600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:85503400-85503600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:85503400-85503600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:85503400-85503600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
36	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
37	chr4:85503400-85503600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr4:85503400-85503600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:85503400-85503600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr4:85503400-85503600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr4:85503400-85503600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:85503400-85503600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:85503400-85503600	Enhancers	Aorta	Aorta
46	chr4:85503400-85503600	Flanking Bivalent TSS/Enh	Liver	Liver
47	chr4:85503400-85503600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr4:85503400-85503600	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr4:85503400-85503600	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr4:85503400-85503600	Active TSS	Colonic Mucosa	Colon

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