Variant report

Variant	rs28768122
Chromosome Location	chr12:123885974-123885975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123879282..123881067-chr12:123885695..123887495,2	MCF-7	breast:
2	chr12:123884955..123886643-chr12:123903886..123905556,2	MCF-7	breast:
3	chr12:123880916..123883261-chr12:123885627..123887999,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10773013	0.82[ASN][1000 genomes]
rs28435460	0.85[ASN][1000 genomes]
rs28509440	0.92[ASN][1000 genomes]
rs28862317	0.93[ASN][1000 genomes]
rs28888731	0.81[ASN][1000 genomes]
rs6488874	0.81[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28768122	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs28768122	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28768122	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28768122	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28768122	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28768122	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28768122	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28768122	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
5	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
7	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:123877400-123889000	Weak transcription	Fetal Heart	heart
10	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:123881400-123886400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:123881600-123887200	Weak transcription	Small Intestine	intestine
13	chr12:123881600-123888200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:123881600-123888400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:123881600-123888600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:123881600-123889000	Weak transcription	Fetal Brain Male	brain
17	chr12:123881800-123886800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:123881800-123887200	Weak transcription	Primary B cells from cord blood	blood
19	chr12:123881800-123888800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:123881800-123889000	Weak transcription	Fetal Kidney	kidney
21	chr12:123882000-123886800	Weak transcription	HepG2	liver
22	chr12:123882000-123888600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:123883400-123886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:123883400-123886400	Weak transcription	Hela-S3	cervix
27	chr12:123883800-123894200	Strong transcription	HUVEC	blood vessel
28	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:123884000-123886400	Weak transcription	NHLF	lung
30	chr12:123884000-123886600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:123884000-123886600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:123884000-123886600	Strong transcription	Fetal Stomach	stomach
33	chr12:123884000-123887800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:123884000-123888800	Weak transcription	Psoas Muscle	Psoas
35	chr12:123884200-123886400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:123884200-123886400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:123884200-123886400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:123884200-123886400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:123884200-123886400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:123884200-123886400	Weak transcription	Left Ventricle	heart
41	chr12:123884200-123886400	Weak transcription	Pancreas	Pancrea
42	chr12:123884200-123886400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:123884200-123886400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:123884200-123886400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:123884200-123886400	Weak transcription	K562	blood
46	chr12:123884200-123886600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:123884200-123886600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:123884200-123886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:123884200-123886600	Weak transcription	Brain Angular Gyrus	brain
50	chr12:123884200-123886600	Weak transcription	Brain Anterior Caudate	brain

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