Variant report

Variant	rs886260
Chromosome Location	chr12:47755374-47755375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46776942..46778519-chr12:47754254..47756489,2	K562	blood:
2	chr12:47747878..47750575-chr12:47752854..47757674,4	MCF-7	breast:
3	chr12:47753767..47756781-chr12:47759547..47762468,3	K562	blood:
4	chr12:47753699..47756781-chr12:47760392..47762468,4	K562	blood:
5	chr12:47608234..47610845-chr12:47753711..47756598,2	K562	blood:

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000179715	Chromatin interaction
ENSG00000247774	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10748469	0.86[EUR][1000 genomes]
rs10785674	0.86[EUR][1000 genomes]
rs10785676	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10881095	0.86[EUR][1000 genomes]
rs10881097	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1421355	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58058166	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6582705	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969338	0.86[CHB][hapmap];0.92[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs886260	HDAC7	cis	parietal	SCAN
rs886260	C12orf41	cis	cerebellum	SCAN
rs886260	RPAP3	cis	parietal	SCAN
rs886260	SLC38A4	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47753600-47755600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:47753600-47756800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr12:47753800-47755600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:47753800-47756800	Enhancers	Fetal Thymus	thymus
5	chr12:47754000-47755600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr12:47754000-47755600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:47754000-47755600	Enhancers	Adipose Nuclei	Adipose
8	chr12:47754000-47755800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:47754000-47756400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:47754200-47755400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:47754200-47755400	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr12:47754200-47755400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:47754200-47755600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:47754400-47755400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr12:47754400-47755400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:47754400-47755400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:47754400-47755400	Active TSS	Duodenum Mucosa	Duodenum
18	chr12:47754400-47755600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:47754400-47755600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr12:47754400-47755600	Flanking Active TSS	Dnd41	blood
21	chr12:47754400-47755600	Flanking Active TSS	K562	blood
22	chr12:47754400-47755800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr12:47754400-47756200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:47754400-47756200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr12:47754400-47756400	Enhancers	A549	lung
26	chr12:47754400-47756600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:47754600-47755400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:47754600-47755400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:47754600-47755400	Enhancers	Spleen	Spleen
30	chr12:47754600-47755600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:47754600-47755600	Enhancers	Placenta	Placenta
32	chr12:47754800-47755400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:47754800-47755400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr12:47754800-47755600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr12:47754800-47755600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr12:47754800-47756200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:47755000-47755400	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:47755000-47755400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr12:47755000-47755400	Flanking Active TSS	NHEK	skin
40	chr12:47755000-47755600	Enhancers	Stomach Mucosa	stomach
41	chr12:47755000-47756400	Enhancers	HUVEC	blood vessel
42	chr12:47755200-47755400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:47755200-47755400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:47755200-47755400	Flanking Active TSS	GM12878-XiMat	blood
45	chr12:47755200-47755400	Flanking Active TSS	HMEC	breast
46	chr12:47755200-47755600	Enhancers	Thymus	Thymus
47	chr12:47755200-47755800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:47755200-47756200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:47755200-47756200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:47755200-47756200	Enhancers	Fetal Intestine Small	intestine

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