Variant report

Variant	rs2722171
Chromosome Location	chr12:104449487-104449488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104448374..104451258-chr12:104456861..104459762,4	K562	blood:

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12369883	1.00[ASN][1000 genomes]
rs2254063	1.00[ASN][1000 genomes]
rs2583271	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583277	1.00[ASN][1000 genomes]
rs2629779	1.00[ASN][1000 genomes]
rs2629793	0.93[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2629804	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2700510	1.00[ASN][1000 genomes]
rs2700515	1.00[ASN][1000 genomes]
rs2722169	1.00[ASN][1000 genomes]
rs2723845	0.87[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723846	1.00[ASN][1000 genomes]
rs2723847	1.00[ASN][1000 genomes]
rs2723868	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2722171	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104444400-104457400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:104444600-104449600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:104444600-104449600	Weak transcription	Fetal Lung	lung
4	chr12:104444600-104449600	Weak transcription	HSMM	muscle
5	chr12:104444600-104449600	Weak transcription	HSMMtube	muscle
6	chr12:104444600-104449800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:104444600-104449800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:104444600-104451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:104444600-104451600	Weak transcription	HMEC	breast
10	chr12:104444800-104452600	Weak transcription	Placenta	Placenta
11	chr12:104448200-104449600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:104448400-104449600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:104448400-104449600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr12:104448400-104450600	Enhancers	Fetal Muscle Leg	muscle
15	chr12:104448400-104450800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:104448600-104449600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:104448600-104449600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:104448600-104449800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:104448600-104450200	Enhancers	Fetal Muscle Trunk	muscle
20	chr12:104448800-104449600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:104448800-104450800	Enhancers	Colon Smooth Muscle	Colon
22	chr12:104448800-104451800	Weak transcription	NHEK	skin
23	chr12:104449000-104449600	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:104449000-104450000	Enhancers	Fetal Brain Female	brain
25	chr12:104449000-104450200	Enhancers	Ovary	ovary
26	chr12:104449000-104450200	Enhancers	Pancreas	Pancrea
27	chr12:104449000-104450400	Enhancers	Stomach Smooth Muscle	stomach
28	chr12:104449000-104450600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:104449000-104452000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:104449200-104449800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:104449200-104449800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:104449200-104450200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:104449200-104450400	Enhancers	NHLF	lung
34	chr12:104449200-104450400	Enhancers	Osteobl	bone
35	chr12:104449200-104450800	Enhancers	Fetal Heart	heart
36	chr12:104449200-104450800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:104449200-104451600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:104449200-104451800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:104449400-104450400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:104449400-104450600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:104449400-104451200	Enhancers	Liver	Liver
42	chr12:104449400-104451800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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