Variant report

Variant	rs537412038
Chromosome Location	chr1:228192427-228192428
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	MAX	chr1:228191779-228193032	H1-hESC	embryonic stem cell:	n/a	chr1:228192400-228192419 chr1:228192404-228192414 chr1:228192403-228192412 chr1:228192403-228192418 chr1:228192979-228192989 chr1:228192405-228192414 chr1:228192406-228192415
2	SMC3	chr1:228191851-228192693	SK-N-SH	brain:	n/a	chr1:228192156-228192170 chr1:228192629-228192639
3	RAD21	chr1:228191946-228192483	MCF-7	breast:	n/a	n/a
4	RAD21	chr1:228191919-228192445	MCF-7	breast:	n/a	n/a
5	USF2	chr1:228191997-228192925	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:228191791-228192458	MCF-7	breast:	n/a	chr1:228192154-228192172 chr1:228192157-228192170 chr1:228192155-228192171
7	USF1	chr1:228192134-228192987	H1-hESC	embryonic stem cell:	n/a	chr1:228192755-228192766
8	SIN3A	chr1:228191993-228192871	H1-hESC	embryonic stem cell:	n/a	chr1:228192219-228192227 chr1:228192333-228192346
9	USF2	chr1:228192377-228192569	GM12878	blood:	n/a	n/a
10	USF1	chr1:228192241-228192604	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr1:228191779-228193003	H1-hESC	embryonic stem cell:	n/a	chr1:228192400-228192419 chr1:228192404-228192414 chr1:228192403-228192412 chr1:228192403-228192418 chr1:228192979-228192989 chr1:228192405-228192414 chr1:228192406-228192415
12	CTCF	chr1:228191767-228192492	SK-N-SH	brain:	n/a	chr1:228192154-228192172 chr1:228192157-228192170 chr1:228192155-228192171
13	CTBP2	chr1:228191942-228194483	H1-hESC	embryonic stem cell:	n/a	n/a
14	MXI1	chr1:228191994-228192457	H1-hESC	embryonic stem cell:	n/a	chr1:228192404-228192413
15	CTCF	chr1:228191852-228192602	HCT-116	colon:	n/a	chr1:228192154-228192172 chr1:228192157-228192170 chr1:228192155-228192171 chr1:228192546-228192559
16	MYC	chr1:228192353-228192495	H1-hESC	embryonic stem cell:	n/a	chr1:228192400-228192419 chr1:228192404-228192414 chr1:228192403-228192412 chr1:228192403-228192418 chr1:228192405-228192414 chr1:228192406-228192415
17	RAD21	chr1:228191948-228192469	HCT-116	colon:	n/a	n/a
18	RAD21	chr1:228191873-228192452	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr1:228191847-228192428	A549	lung:	n/a	n/a
20	CTCF	chr1:228191980-228192512	A549	lung:	n/a	chr1:228192154-228192172 chr1:228192157-228192170 chr1:228192155-228192171
21	TBP	chr1:228192066-228192658	H1-hESC	embryonic stem cell:	n/a	n/a
22	BRCA1	chr1:228192045-228192445	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:228192036-228192465	K562	blood:	n/a	chr1:228192154-228192172 chr1:228192157-228192170 chr1:228192155-228192171

No.	Distal block	Cell Line	Cell type
1	chr1:228183425..228185730-chr1:228191246..228193322,2	K562	blood:
2	chr1:228191350..228193786-chr1:228257693..228259549,2	MCF-7	breast:
3	chr1:228190330..228192732-chr1:228296220..228298722,2	MCF-7	breast:
4	chr1:228191198..228193021-chr1:228266290..228268211,2	MCF-7	breast:
5	chr1:228191745..228192555-chr1:228261259..228261971,3	MCF-7	breast:
6	chr1:228191411..228193255-chr1:228202404..228204319,2	MCF-7	breast:
7	chr1:228185587..228188986-chr1:228190632..228193211,3	MCF-7	breast:
8	chr1:228190431..228192672-chr1:228192836..228195791,3	K562	blood:
9	chr1:228192133..228194243-chr1:228287809..228289393,2	K562	blood:
10	chr1:228191722..228192636-chr1:228703111..228703660,2	K562	blood:
11	chr1:228190036..228193608-chr1:228195528..228197492,3	MCF-7	breast:
12	chr1:228191286..228192801-chr1:228197982..228200475,2	K562	blood:
13	chr1:228190941..228192847-chr1:228260763..228262214,8	MCF-7	breast:
14	chr1:228191780..228193444-chr1:228317568..228320348,2	MCF-7	breast:
15	chr1:228184192..228186220-chr1:228191479..228194171,2	MCF-7	breast:
16	chr1:228191722..228192673-chr1:228250185..228251379,8	MCF-7	breast:
17	chr1:228190517..228193309-chr1:228296399..228298991,3	K562	blood:
18	chr1:228191215..228193545-chr1:228195515..228198090,2	MCF-7	breast:
19	chr1:228191659..228192604-chr1:228250180..228251187,13	MCF-7	breast:
20	chr1:228191736..228192588-chr1:228261257..228262099,3	K562	blood:
21	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:

Variant related genes	Relation type
WNT3A	TF binding region
ENSG00000154342	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228191000-228194400	Weak transcription	Right Atrium	heart
2	chr1:228191800-228193000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
3	chr1:228191800-228193200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:228191800-228193800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr1:228191800-228194000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228191800-228194200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:228192000-228192600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:228192000-228192800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr1:228192000-228192800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:228192000-228192800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
11	chr1:228192000-228192800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr1:228192000-228193200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr1:228192000-228194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:228192000-228194600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:228192000-228194600	Bivalent Enhancer	Fetal Stomach	stomach
16	chr1:228192200-228192600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:228192200-228192600	Bivalent Enhancer	HepG2	liver
18	chr1:228192200-228192800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr1:228192200-228192800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr1:228192200-228192800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:228192200-228192800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr1:228192200-228192800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr1:228192200-228193000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr1:228192200-228193000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
25	chr1:228192200-228193600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:228192200-228194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:228192200-228196800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:228192400-228192600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
29	chr1:228192400-228192600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:228192400-228192600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:228192400-228192600	Bivalent Enhancer	NHEK	skin
32	chr1:228192400-228192800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr1:228192400-228192800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr1:228192400-228192800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:228192400-228192800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
36	chr1:228192400-228192800	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr1:228192400-228192800	Bivalent Enhancer	Brain Anterior Caudate	brain
38	chr1:228192400-228192800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr1:228192400-228193800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
40	chr1:228192400-228195200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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