Variant report

Variant	rs799261
Chromosome Location	chr12:56924389-56924390
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56920527..56922162-chr12:56923065..56925052,2	K562	blood:
2	chr12:56916433..56918956-chr12:56923495..56926214,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2638287	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2638301	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2657896	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657907	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2694917	0.88[AMR][1000 genomes]
rs2694919	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2933235	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs774211	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774215	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs799260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs813497	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs799261	SPRYD4	cis	multi-tissue	Pritchard
rs799261	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56917000-56958000	Weak transcription	Ovary	ovary
3	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:56917400-56924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
7	chr12:56918600-56930000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:56919400-56929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:56920600-56924800	Enhancers	Placenta	Placenta
10	chr12:56921200-56924400	Weak transcription	HSMMtube	muscle
11	chr12:56921200-56930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:56921400-56933400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:56921400-56956200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:56922000-56924600	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:56922000-56924800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:56922000-56933000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:56922000-56935400	Weak transcription	Fetal Lung	lung
18	chr12:56922200-56928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:56922400-56925000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:56922400-56956200	Weak transcription	HSMM	muscle
21	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
22	chr12:56922800-56924400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:56922800-56924600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:56922800-56925000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:56923000-56924800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:56923200-56924800	Enhancers	NHDF-Ad	bronchial
27	chr12:56923200-56949200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:56923400-56924600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:56923400-56926600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:56923400-56926800	Weak transcription	Fetal Stomach	stomach
31	chr12:56923400-56926800	Weak transcription	Left Ventricle	heart
32	chr12:56923400-56929600	Weak transcription	Fetal Intestine Small	intestine
33	chr12:56923400-56931200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:56923600-56924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:56923600-56924400	Weak transcription	NHLF	lung
36	chr12:56923600-56930800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:56923600-56931200	Weak transcription	Osteobl	bone
38	chr12:56923600-56933000	Weak transcription	NHEK	skin
39	chr12:56923800-56925200	Enhancers	Hela-S3	cervix
40	chr12:56923800-56926800	Weak transcription	Lung	lung
41	chr12:56923800-56928400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:56923800-56930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:56923800-56931000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:56923800-56931000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:56923800-56938800	Weak transcription	HMEC	breast
46	chr12:56923800-56959400	Weak transcription	Aorta	Aorta
47	chr12:56924000-56926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:56924000-56930400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:56924200-56924400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:56924200-56924400	Enhancers	Fetal Muscle Leg	muscle

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