Variant report

Variant	rs529582
Chromosome Location	chr1:85929008-85929009
allele	A/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	POLR2A	chr1:85928502-85932579	HUVEC	blood vessel:	n/a	n/a
2	YY1	chr1:85928879-85929183	HepG2	liver:	n/a	chr1:85929032-85929040 chr1:85929085-85929104 chr1:85929027-85929044
3	TCF7L2	chr1:85928716-85930001	PANC-1	pancreas:	n/a	chr1:85929197-85929211 chr1:85929199-85929208 chr1:85929196-85929212 chr1:85929200-85929209 chr1:85929198-85929208 chr1:85929196-85929212
4	POLR2A	chr1:85928241-85929046	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:85928236-85932598	HUVEC	blood vessel:	n/a	n/a
6	STAT3	chr1:85928937-85929107	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:85928257-85932490	HUVEC	blood vessel:	n/a	n/a
8	TCF7L2	chr1:85928952-85929545	HEK293	kidney:	n/a	chr1:85929197-85929211 chr1:85929199-85929208 chr1:85929196-85929212 chr1:85929200-85929209 chr1:85929198-85929208 chr1:85929196-85929212
9	TCF7L2	chr1:85928851-85929778	HepG2	liver:	n/a	chr1:85929197-85929211 chr1:85929199-85929208 chr1:85929196-85929212 chr1:85929200-85929209 chr1:85929198-85929208 chr1:85929196-85929212
10	POLR2A	chr1:85928095-85932547	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:85928913-85932472	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:85928110-85932105	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85920031..85922123-chr1:85928283..85929923,2	K562	blood:
2	chr1:85927983..85931587-chr1:86046693..86050651,4	MCF-7	breast:
3	chr1:85917225..85920485-chr1:85926526..85929082,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273264	TF binding region
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1241320	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389112	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36104818	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs527762	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597168	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61223539	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61783057	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:85917400-85929400	Weak transcription	Gastric	stomach
3	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
4	chr1:85920000-85929600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:85923200-85929800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:85925000-85929200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:85925200-85929400	Weak transcription	Aorta	Aorta
8	chr1:85925400-85929200	Weak transcription	Adipose Nuclei	Adipose
9	chr1:85925800-85929200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:85926400-85929200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:85926400-85929400	Weak transcription	NHEK	skin
12	chr1:85926600-85929400	Weak transcription	Ovary	ovary
13	chr1:85926600-85929400	Weak transcription	HMEC	breast
14	chr1:85926800-85929800	Weak transcription	Placenta	Placenta
15	chr1:85927000-85929200	Flanking Active TSS	HepG2	liver
16	chr1:85927800-85929400	Flanking Active TSS	HUVEC	blood vessel
17	chr1:85928000-85929200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:85928000-85929200	Weak transcription	Fetal Lung	lung
19	chr1:85928200-85929400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr1:85928200-85929600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:85928200-85931000	Active TSS	NHLF	lung
22	chr1:85928400-85929200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:85928400-85929400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:85928400-85929400	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:85928400-85929800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:85928400-85929800	Enhancers	Small Intestine	intestine
27	chr1:85928400-85929800	Flanking Active TSS	Osteobl	bone
28	chr1:85928400-85931400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:85928400-85931600	Active TSS	Brain Anterior Caudate	brain
30	chr1:85928600-85929200	Active TSS	Brain Germinal Matrix	brain
31	chr1:85928600-85929200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:85928600-85929200	Enhancers	A549	lung
33	chr1:85928600-85929400	Weak transcription	Pancreas	Pancrea
34	chr1:85928600-85929600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:85928600-85929800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:85928600-85931600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:85928800-85929200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:85928800-85929200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:85928800-85929200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:85928800-85929400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:85928800-85929600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr1:85928800-85929800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:85928800-85929800	Active TSS	Brain Hippocampus Middle	brain
44	chr1:85928800-85929800	Weak transcription	Lung	lung
45	chr1:85928800-85931200	Active TSS	Liver	Liver
46	chr1:85928800-85931400	Active TSS	Duodenum Mucosa	Duodenum
47	chr1:85929000-85929200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr1:85929000-85929200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:85929000-85929200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr1:85929000-85929200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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