Variant report

Variant	rs28683528
Chromosome Location	chr12:123845351-123845352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123844957-123845676	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
2	chr12:123844945..123846829-chr12:123847352..123848905,2	MCF-7	breast:
3	chr12:123829057..123831002-chr12:123845125..123847852,2	K562	blood:
4	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
5	chr12:123844989..123847500-chr12:124065839..124068689,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256092	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1060105	0.86[EUR][1000 genomes]
rs10773008	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10846515	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11057270	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11830103	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12298826	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12299125	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12304248	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12316131	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12322888	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28372579	0.87[EUR][1000 genomes]
rs28406193	0.86[EUR][1000 genomes]
rs28413626	0.89[EUR][1000 genomes]
rs28458312	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28472704	0.86[EUR][1000 genomes]
rs28576953	0.86[EUR][1000 genomes]
rs28582096	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28583837	0.93[EUR][1000 genomes]
rs28592876	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28636834	0.92[EUR][1000 genomes]
rs28675824	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28809230	0.91[EUR][1000 genomes]
rs28855757	0.83[EUR][1000 genomes]
rs34997336	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759420	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67624109	0.89[EUR][1000 genomes]
rs7485502	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7955457	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7980687	0.89[EUR][1000 genomes]
rs9300255	0.84[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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28683528	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28683528	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28683528	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28683528	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28683528	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28683528	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28683528	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28683528	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28683528	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
3	chr12:123820400-123847000	Weak transcription	Fetal Brain Male	brain
4	chr12:123829000-123847400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:123830000-123847400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:123830000-123847400	Weak transcription	Colonic Mucosa	Colon
7	chr12:123830000-123847400	Weak transcription	NHLF	lung
8	chr12:123830200-123847400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:123830200-123847400	Weak transcription	NHDF-Ad	bronchial
10	chr12:123830200-123847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:123830400-123847600	Weak transcription	Aorta	Aorta
12	chr12:123830600-123847600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:123830800-123846600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:123830800-123847200	Weak transcription	Hela-S3	cervix
15	chr12:123830800-123847200	Weak transcription	HSMMtube	muscle
16	chr12:123832400-123848200	Weak transcription	Esophagus	oesophagus
17	chr12:123832600-123846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:123832600-123846600	Weak transcription	Spleen	Spleen
19	chr12:123832800-123847000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:123832800-123847000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:123832800-123847200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:123832800-123847400	Weak transcription	Osteobl	bone
23	chr12:123832800-123847800	Weak transcription	Fetal Kidney	kidney
24	chr12:123833000-123847000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:123833000-123847000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:123833800-123847600	Weak transcription	NH-A	brain
27	chr12:123834000-123847000	Weak transcription	Adipose Nuclei	Adipose
28	chr12:123834200-123847000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:123834200-123847400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:123834200-123847400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:123834200-123847400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:123834400-123846400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:123834600-123847400	Weak transcription	NHEK	skin
34	chr12:123834800-123846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:123834800-123847000	Weak transcription	Placenta	Placenta
36	chr12:123834800-123847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:123835000-123847400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:123835000-123847400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:123835000-123847400	Weak transcription	Thymus	Thymus
40	chr12:123835000-123847800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:123835000-123848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:123835200-123847600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:123835400-123847400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:123835400-123847800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:123835400-123847800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:123836000-123848200	Weak transcription	Gastric	stomach
47	chr12:123837400-123847200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:123837800-123847000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:123838800-123847400	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:123839200-123845800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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