Variant report

Variant	rs55653628
Chromosome Location	chr1:228652760-228652761
allele	A/C
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	FOXM1	chr1:228652061-228652787	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:228651872-228652857	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr1:228652464-228652889	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:228651122-228652770	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:228651231-228652786	GM12878	blood:	n/a	n/a
6	PML	chr1:228650982-228652818	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:228652158-228653270	H1-neurons	neurons:	n/a	n/a
8	TAF1	chr1:228651734-228652815	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr1:228651232-228652778	IMR90	lung:	n/a	n/a
10	SIN3A	chr1:228651316-228653186	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr1:228652152-228652904	H1-neurons	neurons:	n/a	n/a
12	CTCF	chr1:228652640-228652790	HBMEC	blood vessel:	n/a	n/a
13	REST	chr1:228651155-228653442	H1-neurons	neurons:	n/a	n/a
14	MAX	chr1:228652187-228652770	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:228651218-228652760	GM19099	blood:	n/a	n/a
16	POLR2A	chr1:228650875-228652956	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:228651271-228652776	GM15510	blood:	n/a	n/a
18	MXI1	chr1:228650409-228653776	SK-N-SH	brain:	n/a	n/a
19	YY1	chr1:228652192-228652767	GM12891	blood:	n/a	chr1:228652352-228652360 chr1:228652348-228652360 chr1:228652410-228652421
20	TAF1	chr1:228652211-228652944	H1-neurons	neurons:	n/a	n/a
21	RFX5	chr1:228652020-228653830	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:228651203-228652826	GM12892	blood:	n/a	n/a
23	NRF1	chr1:228652195-228653019	SK-N-SH	brain:	n/a	chr1:228652504-228652513
24	TCF7L2	chr1:228652672-228653004	PANC-1	pancreas:	n/a	chr1:228652801-228652810 chr1:228652798-228652814 chr1:228652798-228652814 chr1:228652799-228652813
25	SIN3AK20	chr1:228651239-228652773	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:228652152-228653256	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228652493..228655065-chr1:228656279..228659196,2	MCF-7	breast:

Variant related genes	Relation type
HIST3H2BA	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs56369647	1.00[AMR][1000 genomes]
rs6657614	1.00[AMR][1000 genomes]
rs74141329	1.00[AMR][1000 genomes]
rs74144513	1.00[AMR][1000 genomes]

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	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
2	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
3	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
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
11	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228651000-228653000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:228651000-228653200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:228651200-228652800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr1:228651200-228652800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
5	chr1:228651200-228653000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:228651200-228653000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:228651200-228653000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr1:228651200-228653000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:228651200-228653000	Bivalent/Poised TSS	NHLF	lung
10	chr1:228651200-228653200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:228651200-228653200	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr1:228651200-228653400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:228651400-228652800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
14	chr1:228651400-228652800	Bivalent Enhancer	Placenta	Placenta
15	chr1:228651400-228652800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr1:228651400-228652800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr1:228651400-228652800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr1:228651400-228653000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:228651400-228653000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
20	chr1:228651400-228653000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr1:228651600-228652800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:228651600-228652800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr1:228651600-228653000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:228651600-228653000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
25	chr1:228651600-228653000	Bivalent/Poised TSS	NHDF-Ad	bronchial
26	chr1:228651600-228653600	Bivalent Enhancer	Lung	lung
27	chr1:228651800-228652800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:228651800-228652800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:228651800-228652800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:228651800-228652800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:228651800-228652800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
32	chr1:228651800-228652800	Bivalent/Poised TSS	Colonic Mucosa	Colon
33	chr1:228651800-228652800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
34	chr1:228651800-228652800	Active TSS	GM12878-XiMat	blood
35	chr1:228651800-228652800	Bivalent/Poised TSS	HSMMtube	muscle
36	chr1:228651800-228653000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:228652000-228652800	Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:228652000-228652800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr1:228652000-228652800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:228652000-228652800	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr1:228652000-228652800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
42	chr1:228652000-228653000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:228652000-228653000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
44	chr1:228652000-228653000	Active TSS	Brain Anterior Caudate	brain
45	chr1:228652000-228653000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:228652000-228653000	Active TSS	Brain Substantia Nigra	brain
47	chr1:228652000-228653000	Active TSS	Fetal Brain Female	brain
48	chr1:228652000-228653000	Active TSS	Right Atrium	heart
49	chr1:228652000-228653000	Bivalent/Poised TSS	NH-A	brain
50	chr1:228652000-228653200	Active TSS	Right Ventricle	heart

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