Variant report

Variant	rs542457120
Chromosome Location	chr1:228194734-228194735
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	GABPA	chr1:228194710-228195210	H1-hESC	embryonic stem cell:	n/a	chr1:228194940-228194949
2	GABPA	chr1:228194695-228195040	H1-hESC	embryonic stem cell:	n/a	chr1:228194940-228194949
3	ZBTB7A	chr1:228194691-228195139	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228193720..228196616-chr1:228296879..228298469,2	MCF-7	breast:
2	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:

Variant related genes	Relation type
WNT3A	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv826953	chr1:228191929-228196867	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3345664	chr1:228193354-228196202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3391367	chr1:228193679-228195777	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228192200-228196800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:228192400-228195200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
3	chr1:228192800-228194800	Bivalent Enhancer	Placenta	Placenta
4	chr1:228193400-228196600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:228193600-228195000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:228193600-228196200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
7	chr1:228193800-228195200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:228193800-228195200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr1:228193800-228195600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:228193800-228196800	Enhancers	Primary B cells from cord blood	blood
11	chr1:228194000-228194800	Enhancers	Pancreas	Pancrea
12	chr1:228194000-228195000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:228194000-228195000	Bivalent Enhancer	Spleen	Spleen
14	chr1:228194000-228196000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:228194000-228196000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:228194000-228196600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
17	chr1:228194200-228194800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:228194200-228194800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:228194200-228194800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:228194200-228194800	Bivalent/Poised TSS	Psoas Muscle	Psoas
21	chr1:228194200-228194800	Bivalent Enhancer	HMEC	breast
22	chr1:228194200-228194800	Bivalent/Poised TSS	NHEK	skin
23	chr1:228194200-228195000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr1:228194200-228195000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:228194200-228195000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr1:228194200-228195000	Bivalent Enhancer	Lung	lung
27	chr1:228194200-228195400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr1:228194200-228195600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:228194200-228195600	Enhancers	Liver	Liver
30	chr1:228194200-228196600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:228194200-228197400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:228194400-228194800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:228194400-228194800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:228194400-228194800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:228194400-228194800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:228194400-228194800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:228194400-228194800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:228194400-228194800	Bivalent/Poised TSS	Esophagus	oesophagus
39	chr1:228194400-228195000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:228194400-228195000	Active TSS	Right Atrium	heart
41	chr1:228194400-228195000	Bivalent/Poised TSS	Right Ventricle	heart
42	chr1:228194400-228195000	Bivalent/Poised TSS	HSMM	muscle
43	chr1:228194400-228195200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
44	chr1:228194400-228195200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:228194400-228195800	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:228194600-228194800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:228194600-228194800	Bivalent/Poised TSS	Ovary	ovary
48	chr1:228194600-228196000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain

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