Variant report

Variant	rs557918918
Chromosome Location	chr3:42543713-42543714
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	SPI1	chr3:42543523-42543728	K562	blood:	n/a	chr3:42543540-42543547
2	POLR2A	chr3:42543633-42544897	MCF-7	breast:	n/a	n/a
3	SP1	chr3:42543704-42544159	H1-hESC	embryonic stem cell:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
4	JUND	chr3:42543689-42543955	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:42543595-42543778	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr3:42543637-42544293	HepG2	liver:	n/a	n/a
7	TCF7L2	chr3:42543321-42544249	HCT-116	colon:	n/a	n/a
8	SP1	chr3:42543630-42544284	H1-hESC	embryonic stem cell:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
9	BACH1	chr3:42543207-42544084	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP4	chr3:42543662-42544200	H1-hESC	embryonic stem cell:	n/a	chr3:42543995-42544011 chr3:42544077-42544093
11	CTCF	chr3:42543640-42543790	HMEC	breast:	n/a	n/a
12	ATF2	chr3:42543670-42544060	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr3:42543681-42543871	H1-hESC	embryonic stem cell:	n/a	n/a
14	BHLHE40	chr3:42543250-42543741	K562	blood:	n/a	chr3:42543286-42543302
15	MAX	chr3:42543553-42544349	A549	lung:	n/a	n/a
16	MAX	chr3:42543583-42543954	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr3:42543221-42544185	H1-hESC	embryonic stem cell:	n/a	n/a
18	SMC3	chr3:42543179-42543721	SK-N-SH	brain:	n/a	n/a
19	SP1	chr3:42543709-42544311	A549	lung:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
20	E2F6	chr3:42542766-42544628	H1-hESC	embryonic stem cell:	n/a	chr3:42543156-42543166 chr3:42544079-42544088 chr3:42542968-42542978 chr3:42544023-42544032
21	NFYB	chr3:42543624-42544253	K562	blood:	n/a	n/a
22	MAX	chr3:42543544-42544394	ECC-1	luminal epithelium:	n/a	chr3:42544354-42544364
23	POLR2A	chr3:42543663-42544360	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:42543596-42544346	H1-neurons	neurons:	n/a	n/a
25	GABPA	chr3:42543453-42544340	K562	blood:	n/a	chr3:42544170-42544179 chr3:42544120-42544134
26	REST	chr3:42543425-42544258	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr3:42543708-42544327	HCT-116	colon:	n/a	n/a
28	E2F6	chr3:42542720-42544609	H1-hESC	embryonic stem cell:	n/a	chr3:42543156-42543166 chr3:42544079-42544088 chr3:42542968-42542978 chr3:42544023-42544032
29	CTBP2	chr3:42542581-42544333	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr3:42543682-42544715	ECC-1	luminal epithelium:	n/a	chr3:42544354-42544364
31	MAX	chr3:42542801-42544630	H1-hESC	embryonic stem cell:	n/a	chr3:42544354-42544364
32	ZEB1	chr3:42543507-42544358	HepG2	liver:	n/a	n/a
33	SIN3A	chr3:42542545-42544245	H1-hESC	embryonic stem cell:	n/a	chr3:42543175-42543189 chr3:42544122-42544131 chr3:42543460-42543471 chr3:42543617-42543626
34	GATA3	chr3:42543147-42544101	T-47D	breast:	n/a	n/a
35	ELF1	chr3:42543418-42544067	K562	blood:	n/a	n/a
36	RCOR1	chr3:42543226-42544139	K562	blood:	n/a	n/a
37	MAX	chr3:42542424-42544191	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:42542953-42544353	SK-N-SH	brain:	n/a	n/a
39	RAD21	chr3:42543012-42543767	SK-N-SH	brain:	n/a	chr3:42543474-42543483 chr3:42543069-42543079
40	POLR2A	chr3:42543681-42544331	H1-hESC	embryonic stem cell:	n/a	n/a
41	ELF1	chr3:42543211-42544244	GM12878	blood:	n/a	n/a
42	TCF7L2	chr3:42543553-42543743	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr3:42543671-42544814	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr3:42543664-42543823	K562	blood:	n/a	n/a
45	SP1	chr3:42543576-42544342	HCT-116	colon:	n/a	chr3:42544028-42544049 chr3:42544023-42544032 chr3:42543999-42544008 chr3:42544022-42544031 chr3:42543998-42544007 chr3:42544022-42544036 chr3:42543998-42544008 chr3:42543998-42544007 chr3:42544078-42544087 chr3:42544077-42544089 chr3:42543997-42544009 chr3:42543997-42544009 chr3:42544077-42544089 chr3:42544079-42544088 chr3:42544021-42544033 chr3:42544021-42544033
46	ELF1	chr3:42543546-42543791	K562	blood:	n/a	n/a
47	CTCF	chr3:42543660-42543810	NHEK	skin:	n/a	n/a
48	ZEB1	chr3:42543483-42544294	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:42543534-42544608	MCF-7	breast:	n/a	n/a
50	CTCF	chr3:42543640-42543790	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42542597..42545270-chr3:42568668..42571142,2	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3435194	chr3:42543398-42545496	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42542000-42544800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:42542200-42545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:42542400-42544600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:42542600-42544000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
6	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
7	chr3:42542600-42544400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:42542600-42544800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr3:42542600-42545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:42542800-42543800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
16	chr3:42542800-42544000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
19	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
20	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
22	chr3:42542800-42544600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:42542800-42544800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:42543000-42543800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:42543000-42543800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:42543000-42543800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:42543000-42543800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:42543000-42543800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr3:42543000-42543800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:42543000-42543800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr3:42543000-42543800	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr3:42543000-42543800	Bivalent Enhancer	Fetal Brain Male	brain
33	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	Placenta	Placenta
34	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
36	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr3:42543000-42544000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
39	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:42543000-42544000	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
43	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
45	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
46	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
47	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Thymus	Thymus
48	chr3:42543000-42544200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr3:42543000-42544200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:42543000-42544400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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