Variant report

Variant	rs12151994
Chromosome Location	chr21:40690397-40690398
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr21:40689015-40690576	K562	blood:	n/a	n/a
2	JUND	chr21:40690269-40690406	K562	blood:	n/a	n/a
3	ZMIZ1	chr21:40690314-40690613	K562	blood:	n/a	n/a
4	RCOR1	chr21:40690180-40690456	K562	blood:	n/a	n/a
5	POLR2A	chr21:40688736-40691506	Raji	blood:	n/a	n/a
6	TEAD4	chr21:40688942-40690558	K562	blood:	n/a	n/a
7	TBL1XR1	chr21:40689292-40690409	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr21:40689203..40691198-chr21:40730612..40733224,2	MCF-7	breast:
3	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
4	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
5	chr21:40687654..40692063-chr21:40815994..40821163,6	MCF-7	breast:
6	chr21:40689989..40692160-chr21:41044598..41047094,2	MCF-7	breast:
7	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
8	chr21:40689727..40692043-chr21:41693980..41696191,2	MCF-7	breast:

No data

Variant related genes	Relation type
BRWD1	TF binding region
BRWD1-IT2	TF binding region
ENSG00000238556	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1041440	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10427502	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1065242	0.82[AMR][1000 genomes]
rs11910151	0.80[AMR][1000 genomes]
rs12710453	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12710454	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047663	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13047678	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13048178	0.83[AMR][1000 genomes]
rs13049280	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13339986	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13625	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541102	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1984022	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2026265	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2026267	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2150415	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2234543	0.83[AMR][1000 genomes]
rs2735306	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2735309	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2776307	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2776308	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2776309	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28360661	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836933	0.81[AMR][1000 genomes]
rs2836938	0.86[AMR][1000 genomes]
rs2836944	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836953	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836955	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836957	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836964	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836965	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836967	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836968	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836972	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836973	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836974	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836977	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836981	0.85[AFR][1000 genomes]
rs2836982	0.85[AFR][1000 genomes]
rs2989330	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34035316	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34433511	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34578707	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34672724	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34978594	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35068861	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35123057	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35560196	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35571600	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35774464	0.85[ASN][1000 genomes]
rs4818017	0.85[AFR][1000 genomes]
rs55836299	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56306759	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6517523	0.82[AMR][1000 genomes]
rs6517526	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6517527	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6517533	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517538	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66465538	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68004583	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68090597	0.82[AMR][1000 genomes]
rs7277978	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281853	0.83[AFR][1000 genomes]
rs7282624	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283420	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283569	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73221193	0.82[AMR][1000 genomes]
rs7354783	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128026	0.80[AMR][1000 genomes]
rs8128102	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8128620	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128734	0.83[AMR][1000 genomes]
rs8128827	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8128894	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8129147	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8129303	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8129355	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8129416	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130984	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8131965	0.87[AMR][1000 genomes]
rs8133146	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8134733	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941894	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9978775	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12151994	PSMG1	cis	lung	GTEx
rs12151994	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs12151994	PSMG1	cis	Esophagus Mucosa	GTEx
rs12151994	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs12151994	PSMG1	cis	Artery Tibial	GTEx
rs12151994	PSMG1	cis	Muscle Skeletal	GTEx
rs12151994	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40686600-40691400	Enhancers	Primary B cells from peripheral blood	blood
2	chr21:40686800-40690600	Weak transcription	Psoas Muscle	Psoas
3	chr21:40686800-40691200	Weak transcription	Right Ventricle	heart
4	chr21:40686800-40691800	Weak transcription	Right Atrium	heart
5	chr21:40686800-40692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:40687000-40690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40687000-40690600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:40687000-40690600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr21:40687000-40690800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:40687000-40691000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:40687000-40691000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr21:40687000-40691000	Weak transcription	Adipose Nuclei	Adipose
13	chr21:40687000-40691000	Weak transcription	Colon Smooth Muscle	Colon
14	chr21:40687000-40691000	Weak transcription	Hela-S3	cervix
15	chr21:40687000-40691000	Weak transcription	NHLF	lung
16	chr21:40687000-40691200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:40687000-40691200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr21:40687000-40691200	Weak transcription	Pancreas	Pancrea
19	chr21:40687000-40691200	Weak transcription	NHDF-Ad	bronchial
20	chr21:40687000-40691200	Weak transcription	Osteobl	bone
21	chr21:40687000-40691800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr21:40687000-40691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:40687000-40692000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr21:40687000-40693400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr21:40687200-40690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:40687200-40690800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr21:40687200-40690800	Weak transcription	Fetal Muscle Leg	muscle
28	chr21:40687200-40691200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr21:40687200-40691800	Weak transcription	Fetal Stomach	stomach
30	chr21:40687400-40690600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr21:40687600-40693000	Enhancers	Fetal Heart	heart
32	chr21:40688200-40691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr21:40688600-40690400	Weak transcription	HSMMtube	muscle
34	chr21:40688800-40691200	Weak transcription	HSMM	muscle
35	chr21:40689000-40690600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr21:40689000-40690600	Enhancers	HepG2	liver
37	chr21:40689200-40690400	Enhancers	Duodenum Mucosa	Duodenum
38	chr21:40689200-40692000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:40689400-40691200	Weak transcription	A549	lung
40	chr21:40689600-40690400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr21:40689600-40690400	Enhancers	Primary B cells from cord blood	blood
42	chr21:40689600-40690600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr21:40689600-40691200	Enhancers	Fetal Lung	lung
44	chr21:40689600-40692000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:40689600-40693800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr21:40689800-40690600	Weak transcription	Left Ventricle	heart
47	chr21:40689800-40690800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:40689800-40691000	Weak transcription	Liver	Liver
49	chr21:40689800-40691200	Weak transcription	NHEK	skin
50	chr21:40689800-40691800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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