Variant report

Variant	rs2270788
Chromosome Location	chr12:123414349-123414350
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	chr12:123413568..123415277-chr12:123423150..123425253,2	K562	blood:
2	chr12:123409186..123412265-chr12:123414114..123415906,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10847980	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10848076	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11060762	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs11060993	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3782289	0.88[JPT][hapmap]
rs4148857	0.87[JPT][hapmap]
rs4148859	0.88[JPT][hapmap]
rs4534620	0.82[YRI][hapmap]
rs4759362	0.88[JPT][hapmap]
rs7298563	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73230017	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv976725	chr12:123412328-123429898	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123401400-123417200	Weak transcription	Osteobl	bone
2	chr12:123401400-123425200	Weak transcription	Esophagus	oesophagus
3	chr12:123401400-123426000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:123402600-123416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:123402600-123429200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:123402800-123414600	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:123402800-123415400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:123402800-123416400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:123402800-123426600	Weak transcription	NHLF	lung
10	chr12:123402800-123429200	Weak transcription	Gastric	stomach
11	chr12:123402800-123430800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:123403000-123414400	Weak transcription	Right Ventricle	heart
13	chr12:123403000-123416600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:123403000-123426400	Weak transcription	Left Ventricle	heart
15	chr12:123403000-123428800	Weak transcription	Lung	lung
16	chr12:123403000-123444200	Weak transcription	Aorta	Aorta
17	chr12:123403400-123427000	Weak transcription	A549	lung
18	chr12:123405200-123416800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:123405200-123424800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:123405200-123428600	Weak transcription	NHEK	skin
21	chr12:123406800-123415200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:123406800-123417000	Weak transcription	Fetal Lung	lung
23	chr12:123406800-123419800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:123406800-123426600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:123409400-123427600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:123410000-123414600	Weak transcription	Brain Germinal Matrix	brain
27	chr12:123411800-123428800	Weak transcription	Fetal Brain Male	brain
28	chr12:123412000-123415400	Enhancers	Fetal Muscle Trunk	muscle
29	chr12:123412200-123414400	Weak transcription	Spleen	Spleen
30	chr12:123412200-123414600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:123412400-123427200	Weak transcription	Adipose Nuclei	Adipose
32	chr12:123412800-123416600	Weak transcription	GM12878-XiMat	blood
33	chr12:123412800-123427400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:123412800-123431800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:123413000-123418000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:123413200-123415600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:123413200-123417000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:123413200-123418800	Weak transcription	Primary B cells from cord blood	blood
40	chr12:123413200-123424400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:123413400-123415600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:123413400-123416600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:123413400-123419800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:123413400-123425400	Strong transcription	Fetal Brain Female	brain
45	chr12:123413400-123427200	Weak transcription	Small Intestine	intestine
46	chr12:123413400-123427400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:123413400-123427600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:123413400-123427600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:123413600-123416600	Weak transcription	Muscle Satellite Cultured Cells	--

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