Variant report

Variant	rs28690872
Chromosome Location	chr1:153504149-153504150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

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	POLR2A	chr1:153504063-153504327	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:153504009-153509167	U87	brain:	n/a	n/a
5	POLR2A	chr1:153504050-153509343	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:153503811-153509451	U87	brain:	n/a	n/a
7	POLR2A	chr1:153503998-153504260	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:153503817-153509136	U87	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
2	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
3	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
4	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
5	chr1:153489101..153490682-chr1:153503610..153505565,2	MCF-7	breast:
6	chr1:153502325..153505921-chr1:153601540..153604182,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000189171	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	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835413	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]
rs28485860	1.00[AMR][1000 genomes];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[AFR][1000 genomes];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]
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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153489000-153506000	Weak transcription	Gastric	stomach
2	chr1:153495600-153504800	Weak transcription	Spleen	Spleen
3	chr1:153497200-153504600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
5	chr1:153498200-153505200	Weak transcription	Osteobl	bone
6	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
7	chr1:153498400-153504600	Weak transcription	HSMM	muscle
8	chr1:153498400-153504600	Weak transcription	NHDF-Ad	bronchial
9	chr1:153498400-153504800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:153498400-153505400	Weak transcription	HSMMtube	muscle
11	chr1:153498600-153504600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:153498800-153505200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:153498800-153505200	Weak transcription	Right Atrium	heart
14	chr1:153499000-153504200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:153499200-153504600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:153499400-153504200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:153499400-153504200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:153499400-153504200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:153499600-153504600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:153499600-153504800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:153499600-153504800	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:153499600-153505000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:153499600-153505200	Weak transcription	Left Ventricle	heart
24	chr1:153499600-153505200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:153499600-153505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:153499800-153504600	Weak transcription	HepG2	liver
27	chr1:153500000-153504200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:153500000-153504200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:153500000-153504600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:153500000-153504800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:153500000-153504800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:153500000-153504800	Weak transcription	Placenta	Placenta
33	chr1:153500000-153504800	Weak transcription	NHLF	lung
34	chr1:153500000-153505000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:153500200-153504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:153500200-153504200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:153500200-153504200	Weak transcription	Esophagus	oesophagus
38	chr1:153500200-153504600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:153500200-153504600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:153500200-153505200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:153500400-153504200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:153500400-153504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:153500400-153504600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:153500400-153504600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:153500400-153504600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:153500400-153505400	Weak transcription	Fetal Heart	heart
47	chr1:153500600-153504200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:153500600-153504200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:153500600-153504400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:153500600-153504400	Weak transcription	NHEK	skin

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