Variant report

Variant	rs640039
Chromosome Location	chr3:159713846-159713847
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	chr3:159709674..159711926-chr3:159713245..159715321,2	K562	blood:
2	chr3:159710937..159713873-chr3:159714818..159717426,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17826053	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243131	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2561284	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475825	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs568408	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662959	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73025797	0.85[AFR][1000 genomes]

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	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs640039	C3orf57	cis	parietal	SCAN
rs640039	SCARNA7	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159707200-159719400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:159707200-159719600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:159707200-159724200	Weak transcription	Psoas Muscle	Psoas
4	chr3:159707400-159714600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:159707400-159719800	Weak transcription	Primary B cells from cord blood	blood
6	chr3:159707400-159719800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:159707600-159719800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:159708000-159719200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:159708200-159719000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:159708200-159719400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:159708600-159714000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:159708600-159714200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:159708600-159715200	Weak transcription	Spleen	Spleen
14	chr3:159708600-159715400	Weak transcription	Pancreas	Pancrea
15	chr3:159708600-159716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:159709800-159723800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:159710000-159715000	Weak transcription	Left Ventricle	heart
18	chr3:159710200-159714200	Weak transcription	Fetal Intestine Large	intestine
19	chr3:159710600-159714800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:159710600-159715000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:159710800-159714800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:159711600-159714600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:159711600-159724200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:159712000-159729600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:159712200-159714200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:159712200-159718200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:159712200-159718200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:159712200-159721400	Weak transcription	GM12878-XiMat	blood
29	chr3:159712400-159718200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:159712600-159717200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:159712800-159719000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:159712800-159719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:159713000-159718800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:159713000-159734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:159713400-159714000	Weak transcription	NHDF-Ad	bronchial
36	chr3:159713400-159714400	Enhancers	Osteobl	bone
37	chr3:159713400-159719600	Weak transcription	Brain Substantia Nigra	brain
38	chr3:159713400-159721400	Weak transcription	NHLF	lung
39	chr3:159713800-159714400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:159713800-159714400	Enhancers	HSMM	muscle
41	chr3:159713800-159714400	Enhancers	NH-A	brain

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