Variant report

Variant	rs1877153
Chromosome Location	chr1:226313456-226313457
allele	A/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	SMC3	chr1:226312670-226313684	SK-N-SH	brain:	n/a	chr1:226313040-226313054
2	CTCF	chr1:226313380-226313530	BJ	skin:	n/a	n/a
3	REST	chr1:226312969-226313472	A549	lung:	n/a	n/a
4	RAD21	chr1:226312156-226313635	SK-N-SH	brain:	n/a	chr1:226313039-226313058 chr1:226313041-226313048
5	CTCF	chr1:226312586-226313499	HCT-116	colon:	n/a	chr1:226313041-226313054 chr1:226313039-226313055 chr1:226313038-226313056 chr1:226313040-226313061 chr1:226313043-226313051
6	CTCF	chr1:226313380-226313530	NHDF-neo	bronchial:	n/a	n/a
7	RAD21	chr1:226312670-226313468	ECC-1	luminal epithelium:	n/a	chr1:226313039-226313058 chr1:226313041-226313048
8	YY1	chr1:226312823-226313524	H1-hESC	embryonic stem cell:	n/a	chr1:226313012-226313026
9	STAT5A	chr1:226312770-226313525	GM12878	blood:	n/a	n/a
10	CTCF	chr1:226312485-226313635	SK-N-SH	brain:	n/a	chr1:226313041-226313054 chr1:226313039-226313055 chr1:226313038-226313056 chr1:226313040-226313061 chr1:226313043-226313051
11	WRNIP1	chr1:226312842-226313487	GM12878	blood:	n/a	n/a
12	CTCF	chr1:226313360-226313510	NHLF	lung:	n/a	n/a
13	CTCF	chr1:226313320-226313470	BJ	skin:	n/a	n/a
14	RAD21	chr1:226312569-226313551	HCT-116	colon:	n/a	chr1:226313039-226313058 chr1:226313041-226313048
15	MYC	chr1:226313410-226313457	GM12878	blood:	n/a	n/a
16	CTCF	chr1:226311662-226313662	A549	lung:	n/a	chr1:226313041-226313054 chr1:226313039-226313055 chr1:226313038-226313056 chr1:226313040-226313061 chr1:226313043-226313051

No.	Distal block	Cell Line	Cell type
1	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
2	chr1:226311060..226314029-chr1:226383239..226385017,2	MCF-7	breast:
3	chr1:226308185..226314044-chr1:226494990..226498119,7	K562	blood:
4	chr1:226312587..226313584-chr1:226384199..226385318,10	MCF-7	breast:
5	chr1:226310978..226313880-chr1:226320034..226321559,2	K562	blood:
6	chr1:226312574..226313520-chr1:226520859..226521824,5	K562	blood:
7	chr1:226250361..226252761-chr1:226312416..226314743,2	K562	blood:
8	chr1:226313181..226318051-chr1:226333070..226339347,8	MCF-7	breast:
9	chr1:226311771..226313658-chr1:226365752..226368057,2	K562	blood:
10	chr1:226245827..226258736-chr1:226304107..226314743,27	K562	blood:
11	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
12	chr1:226312430..226313509-chr1:226384375..226385354,6	K562	blood:
13	chr1:226312596..226313574-chr1:226388503..226389147,2	K562	blood:
14	chr1:226312693..226313490-chr1:226337264..226338204,2	MCF-7	breast:
15	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
16	chr1:226295676..226301816-chr1:226302378..226313716,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270598	TF binding region
ENSG00000182827	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000183814	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000234478	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10915938	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10915939	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10915940	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12069333	0.94[ASN][1000 genomes]
rs12130296	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12136759	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12145818	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1219671	0.94[ASN][1000 genomes]
rs1877155	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877156	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1877161	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35152719	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3887559	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3892709	0.99[ASN][1000 genomes]
rs4653715	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67947191	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72757092	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9645314	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:226310400-226315200	Weak transcription	HSMMtube	muscle
3	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
4	chr1:226310600-226314600	Weak transcription	Lung	lung
5	chr1:226310600-226315000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:226310600-226315200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:226310600-226315200	Weak transcription	NH-A	brain
8	chr1:226310600-226315400	Weak transcription	HSMM	muscle
9	chr1:226310600-226315400	Weak transcription	HUVEC	blood vessel
10	chr1:226310600-226319800	Weak transcription	Right Ventricle	heart
11	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
12	chr1:226310800-226313600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:226310800-226313600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:226310800-226313600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:226310800-226314600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:226310800-226315200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:226310800-226315200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:226310800-226315400	Weak transcription	Primary T cells from cord blood	blood
19	chr1:226310800-226315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:226311000-226315000	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:226311000-226315200	Enhancers	Primary B cells from cord blood	blood
23	chr1:226311200-226314000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:226311200-226315000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:226311200-226315000	Weak transcription	Placenta	Placenta
26	chr1:226311400-226315000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:226311400-226315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:226311400-226315600	Weak transcription	Liver	Liver
29	chr1:226311400-226315800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:226312000-226315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:226312000-226316400	Weak transcription	Gastric	stomach
32	chr1:226312400-226313600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:226312600-226313600	Enhancers	GM12878-XiMat	blood
34	chr1:226312800-226313600	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:226312800-226313600	Enhancers	Fetal Intestine Large	intestine
36	chr1:226312800-226321000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:226313000-226313600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:226313000-226313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:226313000-226313600	Enhancers	A549	lung
40	chr1:226313000-226314800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:226313000-226314800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:226313000-226314800	Weak transcription	HMEC	breast
43	chr1:226313000-226315000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:226313000-226315000	Weak transcription	Fetal Heart	heart
45	chr1:226313000-226315000	Weak transcription	Fetal Lung	lung
46	chr1:226313000-226315200	Weak transcription	Fetal Kidney	kidney
47	chr1:226313000-226316200	Weak transcription	NHLF	lung
48	chr1:226313000-226316400	Enhancers	Stomach Mucosa	stomach
49	chr1:226313000-226323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:226313200-226315000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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