Variant report

Variant	rs12021809
Chromosome Location	chr1:225941782-225941783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225848350..225851171-chr1:225941340..225944244,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915874	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915875	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12021669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023140	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023665	0.86[CEU][hapmap]
rs12025075	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12025267	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029847	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031637	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12032511	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12034342	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12038476	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039184	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12042000	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042778	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044217	0.94[ASN][1000 genomes]
rs12047520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562612	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1849685	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1857008	0.86[CEU][hapmap]
rs2078389	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3738035	1.00[AFR][1000 genomes]
rs3753650	1.00[AFR][1000 genomes]
rs4557929	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61849043	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61849046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61849047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61851667	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs716966	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225934800-225943200	Weak transcription	Brain Angular Gyrus	brain
2	chr1:225935000-225949600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:225935200-225942800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:225935600-225942600	Weak transcription	Fetal Thymus	thymus
5	chr1:225935600-225942600	Weak transcription	Pancreas	Pancrea
6	chr1:225935800-225942800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:225936000-225942800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:225936000-225942800	Weak transcription	A549	lung
9	chr1:225936200-225943400	Weak transcription	Esophagus	oesophagus
10	chr1:225938400-225942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:225938600-225942600	Weak transcription	Lung	lung
12	chr1:225938600-225945200	Weak transcription	Small Intestine	intestine
13	chr1:225938800-225942800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:225938800-225943200	Weak transcription	Gastric	stomach
15	chr1:225939000-225942600	Weak transcription	Adipose Nuclei	Adipose
16	chr1:225939000-225942800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:225939000-225942800	Weak transcription	Spleen	Spleen
18	chr1:225939200-225942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:225939200-225942600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:225939200-225942800	Weak transcription	Right Atrium	heart
21	chr1:225939200-225949600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:225939400-225943200	Weak transcription	Fetal Kidney	kidney
23	chr1:225939600-225942600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:225939600-225942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:225939600-225942600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:225939600-225942800	Weak transcription	Right Ventricle	heart
27	chr1:225939600-225943400	Weak transcription	Psoas Muscle	Psoas
28	chr1:225939800-225942600	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:225939800-225942600	Weak transcription	Left Ventricle	heart
30	chr1:225939800-225942600	Weak transcription	Ovary	ovary
31	chr1:225939800-225942600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:225939800-225943000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:225939800-225943000	Weak transcription	Fetal Stomach	stomach
34	chr1:225939800-225944800	Enhancers	HepG2	liver
35	chr1:225939800-225945800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:225940000-225942600	Weak transcription	Osteobl	bone
37	chr1:225940000-225943000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:225940000-225943000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:225940000-225943000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:225940000-225943200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:225940200-225942600	Weak transcription	Fetal Lung	lung
42	chr1:225940200-225942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:225940200-225942800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:225940200-225942800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:225940200-225942800	Weak transcription	Fetal Heart	heart
46	chr1:225940200-225943000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:225940200-225943200	Weak transcription	Brain Germinal Matrix	brain
48	chr1:225940400-225942600	Weak transcription	NHLF	lung
49	chr1:225940400-225943000	Weak transcription	Stomach Mucosa	stomach
50	chr1:225941000-225942200	Weak transcription	Placenta	Placenta

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