Variant report

Variant	rs10489340
Chromosome Location	chr1:209798068-209798069
allele	A/C
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	chr1:209797932-209798494	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:209797915-209798121	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:209789528-209798172	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MIR4260	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12073223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12089972	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12090288	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403733	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12410975	1.00[CEU][hapmap]
rs17014889	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014906	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014942	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014955	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17015006	0.82[AMR][1000 genomes]
rs2072937	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072939	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072942	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2076219	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076222	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076232	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076349	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2076350	0.82[EUR][1000 genomes]
rs2076352	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229465	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235542	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.93[ASN][1000 genomes]
rs60927005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs714971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209786800-209800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr1:209787400-209816200	Strong transcription	NHEK	skin
4	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
5	chr1:209791800-209801400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:209792400-209798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209792400-209806400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:209793000-209801600	Enhancers	Ovary	ovary
9	chr1:209793400-209798800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:209793600-209799000	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:209793600-209801600	Enhancers	Spleen	Spleen
12	chr1:209793800-209800000	Weak transcription	Lung	lung
13	chr1:209794000-209799000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:209794200-209798600	Weak transcription	Osteobl	bone
15	chr1:209794200-209799600	Weak transcription	Stomach Mucosa	stomach
16	chr1:209794800-209803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:209795000-209799000	Weak transcription	Fetal Lung	lung
18	chr1:209795200-209799600	Weak transcription	Brain Angular Gyrus	brain
19	chr1:209795200-209804400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:209795400-209799600	Weak transcription	Liver	Liver
21	chr1:209795600-209800800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:209795800-209799000	Weak transcription	Right Atrium	heart
23	chr1:209796000-209798400	Weak transcription	Left Ventricle	heart
24	chr1:209796000-209798600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:209796000-209800800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:209796000-209801000	Weak transcription	Pancreas	Pancrea
27	chr1:209796200-209799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:209796200-209800800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:209796400-209799400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:209796400-209800200	Strong transcription	Colonic Mucosa	Colon
31	chr1:209796400-209800800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:209796400-209801000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:209796800-209799200	Strong transcription	HMEC	breast
34	chr1:209797000-209798400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:209797000-209798400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:209797000-209798400	Strong transcription	Fetal Intestine Large	intestine
37	chr1:209797000-209801400	Enhancers	Fetal Heart	heart
38	chr1:209797000-209801600	Enhancers	Right Ventricle	heart
39	chr1:209797200-209798600	Weak transcription	Esophagus	oesophagus
40	chr1:209797200-209798800	Weak transcription	Gastric	stomach
41	chr1:209797200-209800000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:209797400-209798800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:209797400-209798800	Enhancers	HSMM	muscle
44	chr1:209797400-209799000	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:209797400-209799200	Enhancers	Psoas Muscle	Psoas
46	chr1:209797600-209798200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr1:209797600-209798600	Strong transcription	Fetal Intestine Small	intestine
48	chr1:209797600-209798800	Weak transcription	Fetal Brain Female	brain
49	chr1:209797600-209799000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:209797800-209799200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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