Variant report

Variant	rs12129705
Chromosome Location	chr1:120191044-120191045
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	HEY1	chr1:120190087-120191300	K562	blood:	n/a	chr1:120190738-120190753
2	POLR2A	chr1:120190464-120191307	PANC-1	pancreas:	n/a	n/a
3	STAT3	chr1:120190898-120191063	MCF10A-Er-Src	breast:	n/a	chr1:120190976-120190983
4	E2F6	chr1:120190515-120191270	K562	blood:	n/a	chr1:120190779-120190789 chr1:120190776-120190786 chr1:120191047-120191054 chr1:120190782-120190792
5	CTCF	chr1:120189728-120191607	SK-N-SH	brain:	n/a	chr1:120191378-120191391 chr1:120190990-120191003
6	POLR2A	chr1:120188313-120191533	HUVEC	blood vessel:	n/a	n/a
7	TAF1	chr1:120190462-120191263	HepG2	liver:	n/a	n/a
8	REST	chr1:120189243-120191573	H1-neurons	neurons:	n/a	chr1:120191069-120191076 chr1:120190748-120190761 chr1:120191103-120191116 chr1:120191166-120191179
9	IRF1	chr1:120190736-120191187	K562	blood:	n/a	chr1:120191107-120191121
10	REST	chr1:120190654-120191298	K562	blood:	n/a	chr1:120191069-120191076 chr1:120190748-120190761 chr1:120191103-120191116 chr1:120191166-120191179
11	POLR2A	chr1:120190427-120191407	ProgFib	skin:	n/a	n/a
12	SIN3AK20	chr1:120190218-120191258	PANC-1	pancreas:	n/a	n/a
13	GABPA	chr1:120190699-120191047	Hela-S3	cervix:	n/a	n/a
14	FOS	chr1:120190879-120191121	MCF10A-Er-Src	breast:	n/a	chr1:120191112-120191121
15	MAFF	chr1:120190457-120191070	HepG2	liver:	n/a	n/a
16	JUND	chr1:120190820-120191429	H1-hESC	embryonic stem cell:	n/a	chr1:120191112-120191121
17	ETS1	chr1:120190868-120191074	A549	lung:	n/a	chr1:120190973-120190986 chr1:120190956-120190969 chr1:120190973-120190988 chr1:120190889-120190902
18	POLR2A	chr1:120190460-120191399	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:120190523-120191383	ECC-1	luminal epithelium:	n/a	n/a
20	UBTF	chr1:120190294-120191415	K562	blood:	n/a	n/a
21	SIN3AK20	chr1:120189708-120191464	SK-N-SH	brain:	n/a	n/a
22	YY1	chr1:120190710-120191187	ECC-1	luminal epithelium:	n/a	chr1:120190781-120190795 chr1:120190776-120190787 chr1:120190778-120190792 chr1:120190778-120190787 chr1:120191087-120191098
23	MAX	chr1:120190568-120191319	A549	lung:	n/a	chr1:120191103-120191112
24	SMARCC1	chr1:120189801-120191493	Hela-S3	cervix:	n/a	chr1:120190959-120190968
25	EBF1	chr1:120190508-120191088	GM12878	blood:	n/a	chr1:120190532-120190541 chr1:120190531-120190542
26	POLR2A	chr1:120189786-120191539	HepG2	liver:	n/a	n/a
27	TCF7L2	chr1:120190349-120191274	HCT-116	colon:	n/a	n/a
28	CTCF	chr1:120190940-120191090	NHEK	skin:	n/a	chr1:120190990-120191003
29	ELF1	chr1:120190659-120191294	MCF-7	breast:	n/a	chr1:120190776-120190788 chr1:120190778-120190787
30	GABPA	chr1:120190582-120191458	MCF-7	breast:	n/a	n/a
31	POLR2A	chr1:120190905-120191229	GM12878	blood:	n/a	n/a
32	MXI1	chr1:120189770-120191284	HepG2	liver:	n/a	n/a
33	REST	chr1:120190348-120191289	PFSK-1	brain:	n/a	chr1:120191069-120191076 chr1:120190748-120190761 chr1:120191103-120191116 chr1:120191166-120191179
34	RAD21	chr1:120189732-120191779	SK-N-SH	brain:	n/a	chr1:120191195-120191209 chr1:120190991-120191004
35	MYC	chr1:120188204-120191540	K562	blood:	n/a	chr1:120190213-120190223 chr1:120189879-120189895 chr1:120191103-120191112 chr1:120189705-120189715
36	GABPA	chr1:120190313-120191267	K562	blood:	n/a	n/a
37	TEAD4	chr1:120190660-120191158	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr1:120190490-120191314	PANC-1	pancreas:	n/a	n/a
39	ELF1	chr1:120190107-120191311	GM12878	blood:	n/a	chr1:120190776-120190788 chr1:120190778-120190787
40	MXI1	chr1:120190368-120191301	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr1:120190980-120191130	K562	blood:	n/a	chr1:120190990-120191003
42	MXI1	chr1:120190594-120191318	GM12878	blood:	n/a	n/a
43	RFX5	chr1:120190248-120191583	Hela-S3	cervix:	n/a	chr1:120190963-120190978
44	ELK1	chr1:120190861-120191095	GM12878	blood:	n/a	n/a
45	EP300	chr1:120190294-120191125	GM12878	blood:	n/a	chr1:120190777-120190786 chr1:120191087-120191096 chr1:120190780-120190789 chr1:120190704-120190720
46	POLR2A	chr1:120190154-120191131	H1-hESC	embryonic stem cell:	n/a	n/a
47	GABPA	chr1:120190704-120191175	Hela-S3	cervix:	n/a	n/a
48	IRF1	chr1:120190536-120191625	K562	blood:	n/a	chr1:120191341-120191357 chr1:120191107-120191121
49	TAF1	chr1:120190796-120191251	A549	lung:	n/a	n/a
50	ZBTB33	chr1:120190650-120191311	HCT-116	colon:	n/a	chr1:120191144-120191159

No.	Distal block	Cell Line	Cell type
1	chr1:120190729..120191705-chr13:99228174..99228982,2	Hela-S3	cervix:
2	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
3	chr1:120188687..120197065-chr1:120197482..120205927,19	MCF-7	breast:
4	chr1:120188673..120191126-chr1:120281749..120284526,2	K562	blood:
5	chr1:120188763..120191080-chr1:120201790..120203315,2	K562	blood:
6	chr1:120166768..120169738-chr1:120190505..120193186,2	MCF-7	breast:
7	chr1:120190571..120191183-chr2:55646806..55647748,2	Hela-S3	cervix:
8	chr1:120187998..120191080-chr1:120201790..120203947,3	K562	blood:
9	chr1:120190791..120191303-chr1:235492092..235492913,2	HCT-116	colon:
10	chr1:120190950..120191717-chr11:94706862..94707619,2	HCT-116	colon:
11	chr1:120190883..120191708-chr1:120202673..120203521,2	MCF-7	breast:

Variant related genes	Relation type
ZNF697	TF binding region
ENSG00000186280	Chromatin interaction
ENSG00000102572	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000152904	Chromatin interaction
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10802125	1.00[ASN][1000 genomes]
rs10923868	1.00[ASN][1000 genomes]
rs10923870	1.00[ASN][1000 genomes]
rs11586489	1.00[ASN][1000 genomes]
rs12119140	1.00[ASN][1000 genomes]
rs12121447	1.00[ASN][1000 genomes]
rs12127605	1.00[ASN][1000 genomes]
rs12139088	1.00[ASN][1000 genomes]
rs12144094	1.00[ASN][1000 genomes]
rs17258348	1.00[ASN][1000 genomes]
rs34662109	1.00[ASN][1000 genomes]
rs35821663	1.00[ASN][1000 genomes]
rs4077553	1.00[ASN][1000 genomes]
rs4481896	1.00[ASN][1000 genomes]
rs4659210	1.00[ASN][1000 genomes]
rs56051540	1.00[ASN][1000 genomes]
rs56096705	1.00[ASN][1000 genomes]
rs72695107	1.00[ASN][1000 genomes]
rs72695109	1.00[ASN][1000 genomes]
rs72695117	1.00[ASN][1000 genomes]
rs72695123	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3324852	chr1:120189654-120192402	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120188600-120191600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:120188600-120191600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:120188800-120191400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:120188800-120191600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:120188800-120191600	Active TSS	HSMMtube	muscle
6	chr1:120189200-120191600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:120189200-120191800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:120189200-120191800	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:120189400-120191400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:120189400-120191400	Active TSS	NH-A	brain
11	chr1:120189400-120191600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:120189400-120191600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:120189400-120191600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:120189400-120191800	Active TSS	Right Atrium	heart
15	chr1:120189400-120192000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:120189600-120191400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:120189600-120191400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:120189600-120191400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:120189600-120191400	Active TSS	Fetal Heart	heart
20	chr1:120189600-120191400	Active TSS	Fetal Lung	lung
21	chr1:120189600-120191400	Active TSS	NHEK	skin
22	chr1:120189600-120191400	Active TSS	Osteobl	bone
23	chr1:120189600-120191600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:120189600-120191600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:120189600-120191600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:120189600-120191600	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:120189600-120191600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:120189600-120191600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:120189600-120191600	Active TSS	Fetal Intestine Small	intestine
30	chr1:120189600-120191600	Active TSS	Fetal Kidney	kidney
31	chr1:120189600-120191600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:120189600-120191600	Active TSS	Fetal Stomach	stomach
33	chr1:120189600-120191600	Active TSS	Right Ventricle	heart
34	chr1:120189600-120191600	Bivalent/Poised TSS	HepG2	liver
35	chr1:120189600-120192000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:120189600-120192000	Active TSS	NHLF	lung
37	chr1:120189800-120191400	Active TSS	Brain Substantia Nigra	brain
38	chr1:120189800-120191400	Bivalent/Poised TSS	Fetal Thymus	thymus
39	chr1:120189800-120191600	Active TSS	Colon Smooth Muscle	Colon
40	chr1:120189800-120191600	Active TSS	A549	lung
41	chr1:120189800-120191800	Active TSS	Aorta	Aorta
42	chr1:120190000-120191400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:120190000-120191400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:120190000-120191400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:120190000-120191400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:120190000-120191400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:120190000-120191400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:120190000-120191400	Active TSS	Brain Anterior Caudate	brain
49	chr1:120190000-120191400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:120190000-120191400	Active TSS	Fetal Intestine Large	intestine

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