Variant report

Variant	rs4570678
Chromosome Location	chr12:12617994-12617995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12609394..12612369-chr12:12615599..12621309,5	MCF-7	breast:
2	chr12:12604694..12606790-chr12:12616651..12618443,2	MCF-7	breast:
3	chr12:12617418..12619693-chr12:12712639..12714780,2	MCF-7	breast:
4	chr12:12612821..12616513-chr12:12617624..12619681,3	K562	blood:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction
ENSG00000271370	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11054901	1.00[CEU][hapmap]
rs11054979	0.82[CEU][hapmap]
rs16907998	1.00[ASN][1000 genomes]
rs17312055	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013675	1.00[ASN][1000 genomes]
rs55946646	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188411	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56325045	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56340010	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58809132	1.00[ASN][1000 genomes]
rs61913534	1.00[ASN][1000 genomes]
rs61923612	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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4570678	LOH12CR1	Cis_1M	lymphoblastoid	RTeQTL
rs4570678	LOH12CR1	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:12596000-12620200	Weak transcription	HSMM	muscle
4	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:12597400-12618200	Weak transcription	Gastric	stomach
9	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
11	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:12603200-12618400	Weak transcription	Esophagus	oesophagus
13	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
14	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
16	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:12605200-12618400	Weak transcription	Liver	Liver
18	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney
19	chr12:12608400-12627200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:12608400-12629600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:12609000-12623400	Weak transcription	A549	lung
22	chr12:12609200-12626800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:12609800-12628400	Weak transcription	NHLF	lung
24	chr12:12610000-12618200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:12610200-12618600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:12610200-12620200	Weak transcription	Osteobl	bone
27	chr12:12610400-12618400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:12610800-12622000	Weak transcription	NHEK	skin
29	chr12:12610800-12623000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:12610800-12623200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
32	chr12:12611000-12618400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:12611000-12618600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:12611000-12619400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:12611000-12621600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:12611000-12627800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:12611000-12628600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:12611200-12618200	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:12611200-12620200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:12611200-12622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:12611200-12627400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:12611200-12629000	Weak transcription	Hela-S3	cervix
43	chr12:12611400-12618400	Weak transcription	Brain Anterior Caudate	brain
44	chr12:12611400-12619200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:12611400-12619200	Weak transcription	Adipose Nuclei	Adipose
46	chr12:12611400-12620200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:12611400-12620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:12611400-12620200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:12611400-12620200	Weak transcription	HSMMtube	muscle
50	chr12:12613200-12620800	Weak transcription	Brain Germinal Matrix	brain

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