Variant report

Variant	rs2236890
Chromosome Location	chr1:209794258-209794259
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	EBF1	chr1:209794160-209794437	GM12878	blood:	n/a	chr1:209794330-209794341 chr1:209794279-209794290
2	POLR2A	chr1:209793943-209794682	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:209789528-209798172	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209749002..209750989-chr1:209793739..209796003,2	MCF-7	breast:
2	chr1:209793195..209794900-chr1:209798885..209800894,2	K562	blood:

Variant related genes	Relation type
LAMB3	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10489340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12073223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12089972	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12090288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014889	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014955	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17015006	0.82[AMR][1000 genomes]
rs2072937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072942	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2076219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076349	0.82[EUR][1000 genomes]
rs2076350	0.82[EUR][1000 genomes]
rs2076352	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229465	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235542	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282734	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282736	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282737	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36051870	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58679997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59815577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60927005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs714971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209777800-209796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:209786200-209796200	Strong transcription	HMEC	breast
3	chr1:209786400-209796200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:209786600-209794600	Weak transcription	Pancreas	Pancrea
5	chr1:209786800-209800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:209787200-209795000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr1:209787400-209816200	Strong transcription	NHEK	skin
9	chr1:209788400-209796000	Enhancers	Psoas Muscle	Psoas
10	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
11	chr1:209789200-209794800	Enhancers	Placenta	Placenta
12	chr1:209789200-209795400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:209789200-209795800	Enhancers	Right Atrium	heart
14	chr1:209790200-209797800	Enhancers	Brain Germinal Matrix	brain
15	chr1:209790400-209796000	Enhancers	Right Ventricle	heart
16	chr1:209791200-209795600	Enhancers	HSMMtube	muscle
17	chr1:209791400-209794400	Genic enhancers	Duodenum Mucosa	Duodenum
18	chr1:209791600-209795000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:209791600-209796000	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:209791800-209794800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:209791800-209794800	Enhancers	Fetal Brain Male	brain
22	chr1:209791800-209795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:209791800-209796000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:209791800-209801400	Enhancers	Fetal Muscle Leg	muscle
25	chr1:209792000-209797000	Genic enhancers	Fetal Intestine Large	intestine
26	chr1:209792000-209797600	Genic enhancers	Fetal Intestine Small	intestine
27	chr1:209792200-209795000	Enhancers	Fetal Muscle Trunk	muscle
28	chr1:209792200-209795800	Enhancers	Adipose Nuclei	Adipose
29	chr1:209792400-209798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:209792400-209806400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:209792800-209794600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:209792800-209795800	Weak transcription	Brain Anterior Caudate	brain
33	chr1:209793000-209801600	Enhancers	Ovary	ovary
34	chr1:209793200-209794400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:209793400-209794400	Weak transcription	Left Ventricle	heart
36	chr1:209793400-209795400	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr1:209793400-209798800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:209793600-209794400	Genic enhancers	Fetal Stomach	stomach
39	chr1:209793600-209794600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:209793600-209794600	Enhancers	Fetal Brain Female	brain
41	chr1:209793600-209794800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:209793600-209795000	Enhancers	Fetal Lung	lung
43	chr1:209793600-209795800	Enhancers	Fetal Heart	heart
44	chr1:209793600-209796200	Enhancers	Esophagus	oesophagus
45	chr1:209793600-209797400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:209793600-209799000	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:209793600-209801600	Enhancers	Spleen	Spleen
48	chr1:209793800-209794600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:209793800-209794600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:209793800-209795800	Enhancers	Small Intestine	intestine

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