Variant report

Variant	rs1901428
Chromosome Location	chr2:134400871-134400872
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:134263749..134265675-chr2:134399274..134401241,2	MCF-7	breast:
2	chr2:134383649..134385456-chr2:134399469..134401121,2	MCF-7	breast:
3	chr2:134365245..134367451-chr2:134398214..134401016,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10165896	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10169733	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10171394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10177415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185005	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185520	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192051	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193288	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193374	0.86[ASN][1000 genomes]
rs10193580	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206506	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12328892	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13391014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13393385	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13404176	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13404397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407575	0.93[ASN][1000 genomes]
rs13409971	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13412577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13416986	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419634	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13425366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429974	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827735	0.86[ASN][1000 genomes]
rs1901429	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901432	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901433	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993136	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993137	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084808	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084809	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478058	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28514481	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55646124	0.86[ASN][1000 genomes]
rs57451360	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58763272	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59085210	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60598686	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62177769	0.86[ASN][1000 genomes]
rs62179347	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180296	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180299	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180300	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180302	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180303	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730046	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6733088	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748388	0.96[EUR][1000 genomes]
rs67792617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843232	0.86[ASN][1000 genomes]
rs7422753	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv2934	chr2:134368478-134412454	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv998920	chr2:134382097-134424640	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1901428	CHKA	trans	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134395800-134402800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:134397600-134402000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:134398600-134401000	Enhancers	Osteobl	bone
4	chr2:134398800-134401800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:134398800-134402800	Enhancers	Brain Anterior Caudate	brain
6	chr2:134399000-134401000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:134399200-134401200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:134399200-134402000	Enhancers	Brain Angular Gyrus	brain
9	chr2:134399200-134402000	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:134399400-134401000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:134399400-134401200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:134399400-134401400	Enhancers	Fetal Lung	lung
13	chr2:134399400-134402000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:134399400-134402200	Enhancers	Brain Substantia Nigra	brain
15	chr2:134399400-134416000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:134399800-134401200	Enhancers	Fetal Stomach	stomach
17	chr2:134399800-134402000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:134399800-134402200	Enhancers	Fetal Heart	heart
19	chr2:134399800-134402800	Enhancers	Fetal Brain Male	brain
20	chr2:134400000-134401400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:134400000-134401400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:134400000-134401400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:134400000-134401400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:134400200-134401400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:134400400-134401400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:134400400-134402000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:134400400-134403600	Enhancers	Brain Germinal Matrix	brain
28	chr2:134400400-134407200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:134400600-134402600	Enhancers	Brain Hippocampus Middle	brain
30	chr2:134400800-134401600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:134400800-134402000	Enhancers	Fetal Muscle Leg	muscle
32	chr2:134400800-134403200	Enhancers	Fetal Brain Female	brain

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