Variant report

Variant	rs28485860
Chromosome Location	chr1:153505079-153505080
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	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
2	POLR2A	chr1:153504109-153508508	A549	lung:	n/a	n/a
3	FOXA2	chr1:153505075-153505483	HepG2	liver:	n/a	n/a
4	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
5	FOXA1	chr1:153505074-153505543	HepG2	liver:	n/a	n/a
6	FOXA1	chr1:153505022-153505544	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:153504494-153509551	HCT-116	colon:	n/a	n/a
8	POLR2A	chr1:153504453-153509352	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:153504553-153505111	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:153504672-153509603	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:153504596-153505102	ProgFib	skin:	n/a	n/a
12	POLR2A	chr1:153504009-153509167	U87	brain:	n/a	n/a
13	POLR2A	chr1:153504197-153509314	PBDE	blood:	n/a	n/a
14	CHD1	chr1:153504668-153509572	IMR90	lung:	n/a	n/a
15	SIN3AK20	chr1:153504529-153509673	HCT-116	colon:	n/a	n/a
16	POLR2A	chr1:153504624-153505107	HCT-116	colon:	n/a	n/a
17	ZEB1	chr1:153505051-153505719	HepG2	liver:	n/a	chr1:153505300-153505311
18	GATA1	chr1:153504497-153505858	PBDE	blood:	n/a	chr1:153504737-153504746
19	POLR2A	chr1:153504050-153509343	PANC-1	pancreas:	n/a	n/a
20	FOXA1	chr1:153504979-153505574	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:153503811-153509451	U87	brain:	n/a	n/a
22	POLR2A	chr1:153504771-153509811	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:153504940-153505090	GM12872	blood:	n/a	n/a
24	POLR2A	chr1:153504915-153509447	HCT-116	colon:	n/a	n/a
25	TCF12	chr1:153505017-153510005	A549	lung:	n/a	chr1:153505279-153505288 chr1:153508760-153508770
26	JUN	chr1:153504594-153506726	K562	blood:	n/a	chr1:153506399-153506406 chr1:153504736-153504744
27	ZEB1	chr1:153505039-153506077	HepG2	liver:	n/a	chr1:153505300-153505311
28	POLR2A	chr1:153504484-153509273	IMR90	lung:	n/a	n/a
29	POLR2A	chr1:153503817-153509136	U87	brain:	n/a	n/a
30	POLR2A	chr1:153504661-153505123	HUVEC	blood vessel:	n/a	n/a
31	FOXA1	chr1:153504978-153505561	HepG2	liver:	n/a	n/a
32	FOS	chr1:153504528-153505139	HUVEC	blood vessel:	n/a	chr1:153504734-153504745 chr1:153504736-153504744
33	CTCF	chr1:153504705-153506840	A549	lung:	n/a	chr1:153505773-153505789 chr1:153505476-153505484 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
34	POLR2A	chr1:153504643-153508932	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:153504382-153509132	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr1:153504438-153509047	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
2	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
3	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
4	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
5	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
6	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
7	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
8	chr1:153504209..153505838-chr1:153511280..153513163,2	K562	blood:
9	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
10	chr1:153485879..153486801-chr1:153505033..153505646,2	K562	blood:
11	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
12	chr1:153489101..153490682-chr1:153503610..153505565,2	MCF-7	breast:
13	chr1:153502325..153505921-chr1:153601540..153604182,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000272030	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11488667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11973	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835409	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442251	1.00[EUR][1000 genomes]
rs28451322	1.00[EUR][1000 genomes]
rs28456342	1.00[EUR][1000 genomes]
rs28510499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28605603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28634320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648662	1.00[EUR][1000 genomes]
rs28690872	1.00[AMR][1000 genomes];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[EUR][1000 genomes]
rs56255753	1.00[EUR][1000 genomes]
rs56401460	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]
rs61038462	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	1.00[EUR][1000 genomes]
rs74115478	1.00[EUR][1000 genomes]
rs74115489	1.00[EUR][1000 genomes]
rs746425	1.00[EUR][1000 genomes]
rs7518794	1.00[EUR][1000 genomes]
rs7528738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7543851	1.00[AMR][1000 genomes];1.00[EUR][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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153489000-153506000	Weak transcription	Gastric	stomach
2	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
3	chr1:153498200-153505200	Weak transcription	Osteobl	bone
4	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
5	chr1:153498400-153505400	Weak transcription	HSMMtube	muscle
6	chr1:153498800-153505200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:153498800-153505200	Weak transcription	Right Atrium	heart
8	chr1:153499600-153505200	Weak transcription	Left Ventricle	heart
9	chr1:153499600-153505200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:153499600-153505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:153500200-153505200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:153500400-153505400	Weak transcription	Fetal Heart	heart
13	chr1:153500600-153505200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:153501800-153505600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:153503000-153505400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:153503200-153505200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:153503400-153505400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:153503600-153505200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:153503800-153505400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
22	chr1:153504000-153505200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:153504000-153505200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:153504000-153505200	Enhancers	Dnd41	blood
25	chr1:153504000-153505400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:153504000-153505400	Enhancers	Colonic Mucosa	Colon
27	chr1:153504000-153505400	Enhancers	K562	blood
28	chr1:153504000-153505800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:153504000-153506400	Enhancers	Primary T cells from cord blood	blood
30	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
31	chr1:153504200-153505200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:153504200-153505200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:153504200-153505400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:153504200-153505400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:153504200-153505400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:153504200-153505400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:153504200-153505400	Enhancers	Stomach Mucosa	stomach
38	chr1:153504200-153505400	Enhancers	Thymus	Thymus
39	chr1:153504200-153505800	Enhancers	Esophagus	oesophagus
40	chr1:153504200-153506000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:153504200-153506000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:153504200-153506600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:153504400-153505600	Enhancers	NHEK	skin
45	chr1:153504400-153505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:153504400-153506800	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:153504400-153507000	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:153504600-153505200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr1:153504600-153505200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:153504600-153505200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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