Variant report

Variant	rs477339
Chromosome Location	chr1:153510621-153510622
allele	C/G
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	USF1	chr1:153510526-153511344	HCT-116	colon:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
2	USF1	chr1:153510540-153511223	ECC-1	luminal epithelium:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
3	USF2	chr1:153510572-153511094	K562	blood:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
4	USF1	chr1:153510518-153511332	HCT-116	colon:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
5	USF1	chr1:153510447-153511171	H1-hESC	embryonic stem cell:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
6	USF1	chr1:153510616-153511133	H1-hESC	embryonic stem cell:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
7	USF1	chr1:153510593-153511175	ECC-1	luminal epithelium:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
8	USF1	chr1:153510565-153511226	K562	blood:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927
9	USF2	chr1:153510557-153511295	Hela-S3	cervix:	n/a	chr1:153510912-153510921 chr1:153510912-153510921 chr1:153510910-153510923 chr1:153510911-153510920 chr1:153510911-153510922 chr1:153510906-153510927

No.	Distal block	Cell Line	Cell type
1	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
2	chr1:153509159..153511190-chr1:153606229..153608319,3	K562	blood:
3	chr1:153509922..153512486-chr1:153642550..153644597,2	K562	blood:
4	chr1:153510615..153512174-chr1:153513958..153515590,2	K562	blood:
5	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
6	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
7	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
8	chr1:153508608..153510769-chr1:153600428..153603319,2	K562	blood:
9	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
10	chr1:153508630..153510790-chr1:153606132..153607908,2	K562	blood:

Variant related genes	Relation type
S100A6	TF binding region
ENSG00000196420	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000160678	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16835393	0.92[CEU][hapmap]
rs17695220	0.92[CEU][hapmap]
rs1810765	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1887039	0.92[CEU][hapmap]
rs2094217	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2480695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28483109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762262	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.92[CEU][hapmap]
rs4430277	0.92[CEU][hapmap]
rs4845351	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4845352	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4845554	0.87[CEU][hapmap]
rs532652	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.92[CEU][hapmap]
rs659403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684970	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7518306	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9426945	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153508600-153511600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:153508800-153512600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153509000-153511200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153509000-153511400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:153509200-153511000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:153509200-153512600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:153509200-153512600	Weak transcription	Small Intestine	intestine
8	chr1:153509200-153512800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:153509200-153514000	Enhancers	HMEC	breast
10	chr1:153509200-153515400	Weak transcription	Aorta	Aorta
11	chr1:153509200-153515600	Weak transcription	Fetal Kidney	kidney
12	chr1:153509200-153516800	Enhancers	Fetal Thymus	thymus
13	chr1:153509200-153517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:153509400-153510800	Weak transcription	NH-A	brain
15	chr1:153509400-153510800	Weak transcription	NHLF	lung
16	chr1:153509400-153511000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:153509400-153511000	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:153509400-153511200	Enhancers	Esophagus	oesophagus
19	chr1:153509400-153511200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:153509400-153511400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:153509400-153511600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:153509400-153512800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:153509400-153513000	Weak transcription	GM12878-XiMat	blood
24	chr1:153509400-153513000	Weak transcription	Osteobl	bone
25	chr1:153509400-153513200	Weak transcription	Gastric	stomach
26	chr1:153509400-153515000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:153509400-153515200	Enhancers	NHEK	skin
28	chr1:153509400-153516800	Weak transcription	Right Atrium	heart
29	chr1:153509400-153517000	Weak transcription	HUVEC	blood vessel
30	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:153509600-153510800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:153509600-153511200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:153509600-153511400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:153509600-153511400	Enhancers	A549	lung
35	chr1:153509600-153512000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:153509600-153512000	Weak transcription	Primary T cells from cord blood	blood
37	chr1:153509600-153512000	Weak transcription	HSMM	muscle
38	chr1:153509600-153512200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:153509600-153512200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:153509600-153512400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:153509600-153512600	Weak transcription	HSMMtube	muscle
42	chr1:153509600-153515400	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:153509600-153515400	Weak transcription	Left Ventricle	heart
44	chr1:153509600-153515400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:153509600-153515600	Weak transcription	Fetal Stomach	stomach
46	chr1:153509600-153517000	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:153509800-153510800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:153509800-153510800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:153509800-153510800	Weak transcription	Placenta	Placenta
50	chr1:153509800-153511000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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