Variant report

Variant	rs56056407
Chromosome Location	chr1:212589266-212589267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:212588004-212589288	K562	blood:	n/a	n/a
2	POLR2A	chr1:212587954-212589321	HL-60	blood:	n/a	n/a
3	SREBP1	chr1:212587176-212589923	GM12878	blood:	n/a	n/a
4	JUN	chr1:212586575-212589515	K562	blood:	n/a	chr1:212587985-212587994 chr1:212589466-212589475
5	FOXM1	chr1:212588738-212589362	GM12878	blood:	n/a	n/a
6	FOXM1	chr1:212587882-212589328	GM12878	blood:	n/a	n/a
7	RUNX3	chr1:212587429-212589362	GM12878	blood:	n/a	n/a
8	NR2F2	chr1:212587571-212589354	K562	blood:	n/a	n/a
9	REST	chr1:212588148-212589271	HL-60	blood:	n/a	n/a
10	POLR2A	chr1:212587790-212589312	GM12892	blood:	n/a	n/a
11	RUNX3	chr1:212587943-212589414	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:212587446-212589371	HL-60	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212588338..212589858-chr1:212645243..212647080,2	K562	blood:
2	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
3	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
4	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
5	chr1:212549233..212551182-chr1:212586836..212589324,2	K562	blood:
6	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
7	chr1:212526286..212528256-chr1:212589016..212590996,2	K562	blood:
8	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
9	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000065600	Chromatin interaction
ENSG00000117691	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10157725	1.00[AMR][1000 genomes]
rs10465692	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11571523	1.00[AMR][1000 genomes]
rs11571525	1.00[AMR][1000 genomes]
rs11571531	1.00[AMR][1000 genomes]
rs13375351	1.00[AMR][1000 genomes]
rs1663629	1.00[AMR][1000 genomes]
rs1774254	1.00[AMR][1000 genomes]
rs2921126	1.00[AMR][1000 genomes]
rs3121292	1.00[AMR][1000 genomes]
rs351389	1.00[AMR][1000 genomes]
rs351411	1.00[AMR][1000 genomes]
rs351412	1.00[AMR][1000 genomes]
rs351415	1.00[AMR][1000 genomes]
rs56087556	1.00[AMR][1000 genomes]
rs56160775	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56909493	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57517430	1.00[AMR][1000 genomes]
rs58193366	1.00[AMR][1000 genomes]
rs58843897	1.00[AMR][1000 genomes]
rs59354031	1.00[AMR][1000 genomes]
rs60404556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61460239	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61682449	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs701909	1.00[AMR][1000 genomes]
rs74138106	1.00[AMR][1000 genomes]
rs74138118	1.00[AMR][1000 genomes]
rs74138120	1.00[AMR][1000 genomes]
rs74138121	1.00[AMR][1000 genomes]
rs74138123	1.00[AMR][1000 genomes]
rs74138132	1.00[AMR][1000 genomes]
rs74138133	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138134	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138135	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138136	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138137	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138138	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74138139	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140412	1.00[AMR][1000 genomes]
rs792432	1.00[AMR][1000 genomes]
rs811040	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212588400-212589400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212588400-212590200	Enhancers	Primary hematopoietic stem cells	blood
3	chr1:212588400-212590600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:212588600-212589400	Enhancers	Fetal Thymus	thymus
5	chr1:212588600-212590200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:212588600-212590200	Enhancers	Pancreas	Pancrea
7	chr1:212588600-212595000	Weak transcription	Right Atrium	heart
8	chr1:212588800-212589400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:212588800-212589400	Enhancers	Primary B cells from cord blood	blood
10	chr1:212588800-212589400	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:212588800-212589400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:212588800-212589400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:212588800-212590000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:212588800-212590800	Enhancers	Brain Angular Gyrus	brain
15	chr1:212588800-212591800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:212589000-212589400	Enhancers	Dnd41	blood
17	chr1:212589000-212590200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:212589000-212590400	Enhancers	Brain Anterior Caudate	brain
19	chr1:212589000-212590600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:212589000-212591000	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:212589000-212591000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:212589000-212591400	Enhancers	Brain Substantia Nigra	brain
23	chr1:212589000-212591800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:212589000-212592600	Enhancers	K562	blood
25	chr1:212589200-212589400	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr1:212589200-212589400	Enhancers	GM12878-XiMat	blood
27	chr1:212589200-212589400	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:212589200-212590000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:212589200-212590400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:212589200-212590400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:212589200-212590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:212589200-212590600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:212589200-212591600	Weak transcription	Spleen	Spleen
34	chr1:212589200-212593600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:212589200-212593800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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