Variant report

Variant	rs6440204
Chromosome Location	chr3:143617422-143617423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143615673..143619664-chr3:143688738..143692430,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6440203	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6440204	SCARNA16	trans	cerebellum	SCAN
rs6440204	RASA2	cis	cerebellum	SCAN
rs6440204	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143615000-143617600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:143616200-143617600	Enhancers	NHDF-Ad	bronchial
3	chr3:143616200-143618000	Enhancers	NHLF	lung
4	chr3:143616400-143617600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:143616400-143617600	Enhancers	Brain Angular Gyrus	brain
6	chr3:143616400-143617600	Enhancers	Fetal Lung	lung
7	chr3:143616600-143617600	Enhancers	Fetal Intestine Large	intestine
8	chr3:143616600-143617800	Enhancers	Ovary	ovary
9	chr3:143616800-143617800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:143616800-143617800	Enhancers	Fetal Brain Female	brain
11	chr3:143616800-143618000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:143616800-143619600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:143617000-143617600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:143617000-143617600	Enhancers	Brain Hippocampus Middle	brain
15	chr3:143617000-143617600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:143617000-143618600	Weak transcription	HMEC	breast
17	chr3:143617000-143618800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:143617000-143619000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:143617000-143619600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:143617000-143619600	Weak transcription	NH-A	brain
21	chr3:143617200-143619200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:143617200-143619600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:143617200-143619600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:143617200-143619600	Weak transcription	HSMM	muscle
25	chr3:143617200-143619600	Weak transcription	NHEK	skin
26	chr3:143617200-143619600	Weak transcription	Osteobl	bone
27	chr3:143617400-143617800	Enhancers	Brain Substantia Nigra	brain

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