Variant report

Variant	rs61038462
Chromosome Location	chr1:153538039-153538040
allele	G/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	chr1:153537911-153538756	SK-N-SH	brain:	n/a	n/a
2	REST	chr1:153537934-153538480	A549	lung:	n/a	n/a
3	POLR2A	chr1:153537800-153538783	HCT-116	colon:	n/a	n/a
4	FOSL1	chr1:153537779-153539713	HCT-116	colon:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216 chr1:153539167-153539178
5	STAT3	chr1:153537933-153538810	MCF10A-Er-Src	breast:	n/a	chr1:153538755-153538762
6	POLR2A	chr1:153537976-153539816	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:153537809-153538594	ECC-1	luminal epithelium:	n/a	n/a
8	SP1	chr1:153537979-153539708	A549	lung:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
9	FOSL2	chr1:153537800-153539606	SK-N-SH	brain:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539168-153539179
10	POLR2A	chr1:153537995-153538764	U87	brain:	n/a	n/a
11	SMARCB1	chr1:153537929-153539629	Hela-S3	cervix:	n/a	chr1:153539169-153539178 chr1:153539206-153539215
12	MYC	chr1:153537866-153538660	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:153537876-153538791	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr1:153537829-153539964	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:153537786-153538657	MCF10A-Er-Src	breast:	n/a	n/a
16	MXI1	chr1:153537982-153538540	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:153537999-153538651	PANC-1	pancreas:	n/a	n/a
18	EP300	chr1:153537729-153538708	ECC-1	luminal epithelium:	n/a	n/a
19	MYC	chr1:153537932-153539513	Hela-S3	cervix:	n/a	n/a
20	BCL3	chr1:153537947-153539517	A549	lung:	n/a	n/a
21	FOS	chr1:153537948-153538647	HUVEC	blood vessel:	n/a	chr1:153538365-153538374 chr1:153538363-153538374 chr1:153538361-153538372
22	MAX	chr1:153537957-153538632	SK-N-SH	brain:	n/a	n/a
23	NR3C1	chr1:153537876-153538567	ECC-1	luminal epithelium:	n/a	chr1:153537960-153537967 chr1:153537950-153537963 chr1:153538364-153538373 chr1:153538365-153538374
24	MAZ	chr1:153537646-153539961	IMR90	lung:	n/a	n/a
25	EP300	chr1:153537761-153539602	SK-N-SH	brain:	n/a	chr1:153538969-153538979
26	MYC	chr1:153537844-153539333	MCF10A-Er-Src	breast:	n/a	n/a
27	SP1	chr1:153537910-153539902	A549	lung:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
28	FOXM1	chr1:153537697-153539496	ECC-1	luminal epithelium:	n/a	n/a
29	JUND	chr1:153537838-153539612	HCT-116	colon:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539167-153539178 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216
30	TCF12	chr1:153537812-153539663	SK-N-SH	brain:	n/a	chr1:153539098-153539108 chr1:153537891-153537901 chr1:153539241-153539251
31	NFIC	chr1:153537739-153539631	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:153537804-153539923	HCT-116	colon:	n/a	n/a
33	ZBTB7A	chr1:153537748-153539642	ECC-1	luminal epithelium:	n/a	chr1:153539452-153539460
34	CHD2	chr1:153537966-153538603	Hela-S3	cervix:	n/a	n/a
35	JUND	chr1:153537740-153539749	HCT-116	colon:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539167-153539178 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216
36	POLR2A	chr1:153537968-153539834	HUVEC	blood vessel:	n/a	n/a
37	TEAD4	chr1:153537703-153539867	ECC-1	luminal epithelium:	n/a	n/a
38	MAX	chr1:153537764-153541614	A549	lung:	n/a	chr1:153540434-153540445
39	SP1	chr1:153537781-153539870	HCT-116	colon:	n/a	chr1:153539137-153539146 chr1:153539135-153539146 chr1:153539136-153539150 chr1:153539096-153539110 chr1:153539029-153539043
40	MAX	chr1:153537798-153538757	ECC-1	luminal epithelium:	n/a	n/a
41	E2F6	chr1:153537933-153538805	A549	lung:	n/a	n/a
42	POLR2A	chr1:153537839-153540026	U87	brain:	n/a	n/a
43	FOSL2	chr1:153538020-153538686	A549	lung:	n/a	chr1:153538365-153538374 chr1:153538361-153538372
44	MAX	chr1:153537966-153539552	Hela-S3	cervix:	n/a	n/a
45	HCFC1	chr1:153537823-153539728	Hela-S3	cervix:	n/a	n/a
46	RXRA	chr1:153537933-153539567	SK-N-SH	brain:	n/a	n/a
47	NFIC	chr1:153537700-153539652	ECC-1	luminal epithelium:	n/a	n/a
48	EBF1	chr1:153537740-153539436	GM12878	blood:	n/a	n/a
49	EP300	chr1:153537702-153539693	ECC-1	luminal epithelium:	n/a	chr1:153538969-153538979
50	TCF12	chr1:153537749-153539718	ECC-1	luminal epithelium:	n/a	chr1:153539098-153539108 chr1:153537891-153537901 chr1:153539241-153539251

No.	Distal block	Cell Line	Cell type
1	chr1:153536925..153539179-chr1:153962275..153964605,2	K562	blood:
2	chr1:153535957..153537557-chr1:153537607..153539354,2	MCF-7	breast:
3	chr1:153536879..153538939-chr1:153934770..153936803,2	MCF-7	breast:
4	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
5	chr1:153537152..153539160-chr1:153746062..153748854,2	MCF-7	breast:
6	chr1:153537679..153540436-chr1:153962275..153964884,2	K562	blood:
7	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
8	chr1:153508488..153510083-chr1:153537210..153538800,2	K562	blood:
9	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
10	chr1:153537973..153540755-chr1:153602282..153604926,2	K562	blood:
11	chr1:153514173..153516527-chr1:153537925..153539864,2	K562	blood:
12	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
13	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
14	chr1:153522267..153525133-chr1:153537337..153540137,3	MCF-7	breast:
15	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
16	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
17	chr1:153537683..153540046-chr1:153895076..153896651,2	K562	blood:
18	chr1:153536608..153541746-chr1:153698648..153702694,5	MCF-7	breast:
19	chr1:153536900..153539436-chr1:153605197..153607603,3	K562	blood:
20	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:

Variant related genes	Relation type
S100A2	TF binding region
ENSG00000188015	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11488667	1.00[EUR][1000 genomes]
rs11973	1.00[EUR][1000 genomes]
rs16835357	1.00[EUR][1000 genomes]
rs16835362	1.00[EUR][1000 genomes]
rs16835371	1.00[EUR][1000 genomes]
rs16835373	1.00[EUR][1000 genomes]
rs16835375	1.00[EUR][1000 genomes]
rs16835379	1.00[EUR][1000 genomes]
rs16835389	1.00[EUR][1000 genomes]
rs16835409	1.00[EUR][1000 genomes]
rs16835413	1.00[EUR][1000 genomes]
rs16835417	1.00[EUR][1000 genomes]
rs2104500	1.00[EUR][1000 genomes]
rs2230870	1.00[EUR][1000 genomes]
rs28373144	1.00[EUR][1000 genomes]
rs28407716	1.00[EUR][1000 genomes]
rs28442251	1.00[EUR][1000 genomes]
rs28451322	1.00[EUR][1000 genomes]
rs28456342	1.00[EUR][1000 genomes]
rs28485860	1.00[EUR][1000 genomes]
rs28510499	1.00[EUR][1000 genomes]
rs28578863	1.00[EUR][1000 genomes]
rs28587171	1.00[EUR][1000 genomes]
rs28605603	1.00[EUR][1000 genomes]
rs28634320	1.00[EUR][1000 genomes]
rs28645589	1.00[EUR][1000 genomes]
rs28648662	1.00[EUR][1000 genomes]
rs28690872	1.00[EUR][1000 genomes]
rs28694652	1.00[EUR][1000 genomes]
rs28709866	1.00[EUR][1000 genomes]
rs28784102	1.00[EUR][1000 genomes]
rs3014827	1.00[EUR][1000 genomes]
rs3856025	1.00[EUR][1000 genomes]
rs56140059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56255753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56401460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58529054	1.00[EUR][1000 genomes]
rs59209384	1.00[EUR][1000 genomes]
rs59617976	1.00[EUR][1000 genomes]
rs60219287	1.00[EUR][1000 genomes]
rs60460123	1.00[EUR][1000 genomes]
rs61131911	1.00[EUR][1000 genomes]
rs61148582	1.00[EUR][1000 genomes]
rs73009954	1.00[EUR][1000 genomes]
rs73011738	1.00[EUR][1000 genomes]
rs73020460	1.00[EUR][1000 genomes]
rs73020461	1.00[EUR][1000 genomes]
rs73020464	1.00[EUR][1000 genomes]
rs73020467	1.00[EUR][1000 genomes]
rs73020468	1.00[EUR][1000 genomes]
rs73020471	1.00[EUR][1000 genomes]
rs73020473	1.00[EUR][1000 genomes]
rs73020474	1.00[EUR][1000 genomes]
rs73020478	1.00[EUR][1000 genomes]
rs73020479	1.00[EUR][1000 genomes]
rs73020496	1.00[EUR][1000 genomes]
rs73020497	1.00[EUR][1000 genomes]
rs73024502	1.00[EUR][1000 genomes]
rs73026308	1.00[EUR][1000 genomes]
rs730347	1.00[EUR][1000 genomes]
rs74115477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74115478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74115489	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs746425	1.00[EUR][1000 genomes]
rs7518794	1.00[EUR][1000 genomes]
rs7528738	1.00[EUR][1000 genomes]
rs7543851	1.00[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	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	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
4	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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153532800-153539600	Weak transcription	Thymus	Thymus
2	chr1:153535400-153538400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:153535800-153540800	Enhancers	Fetal Muscle Leg	muscle
4	chr1:153535800-153541600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:153536000-153538600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:153536000-153538800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:153536000-153539200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:153536000-153539200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:153536000-153540800	Enhancers	Fetal Muscle Trunk	muscle
10	chr1:153536000-153541600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:153536000-153541600	Enhancers	Placenta	Placenta
12	chr1:153536000-153541600	Enhancers	Lung	lung
13	chr1:153536000-153542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153536200-153538400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:153536200-153538400	Enhancers	NHLF	lung
16	chr1:153536200-153541800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:153536600-153538200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:153536600-153541000	Enhancers	Fetal Intestine Large	intestine
19	chr1:153536800-153538200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:153536800-153538200	Weak transcription	Gastric	stomach
21	chr1:153536800-153540800	Enhancers	Stomach Mucosa	stomach
22	chr1:153536800-153541800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:153537000-153538200	Enhancers	Fetal Intestine Small	intestine
24	chr1:153537000-153538400	Enhancers	NHDF-Ad	bronchial
25	chr1:153537000-153540800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr1:153537000-153541600	Enhancers	HUVEC	blood vessel
27	chr1:153537200-153538200	Weak transcription	Spleen	Spleen
28	chr1:153537400-153538400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:153537400-153538400	Active TSS	NHEK	skin
30	chr1:153537600-153541600	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:153537800-153538200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:153537800-153538200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:153537800-153538400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:153537800-153538400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr1:153537800-153538400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:153537800-153538400	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:153537800-153538400	Enhancers	HepG2	liver
38	chr1:153537800-153538400	Enhancers	HSMMtube	muscle
39	chr1:153537800-153538600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:153537800-153538600	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:153537800-153538800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:153537800-153538800	Flanking Active TSS	A549	lung
43	chr1:153537800-153539000	Enhancers	Colon Smooth Muscle	Colon
44	chr1:153537800-153539000	Flanking Active TSS	HSMM	muscle
45	chr1:153537800-153539200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:153537800-153539200	Enhancers	Adipose Nuclei	Adipose
47	chr1:153537800-153539200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:153537800-153539200	Enhancers	Osteobl	bone
49	chr1:153537800-153539600	Enhancers	Aorta	Aorta
50	chr1:153537800-153539600	Enhancers	Fetal Stomach	stomach

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