Variant report

Variant	rs10490793
Chromosome Location	chr3:42803280-42803281
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42803200-42803320	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42798882..42800996-chr3:42802140..42804185,2	K562	blood:
2	chr3:42792752..42794704-chr3:42802207..42805435,3	K562	blood:
3	chr3:42796140..42798050-chr3:42801368..42804341,2	K562	blood:

Variant related genes	Relation type
CCDC13	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12635764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12638233	1.00[CEU][hapmap]
rs17074839	1.00[CEU][hapmap]
rs17842066	1.00[CEU][hapmap]
rs28544555	1.00[AFR][1000 genomes]
rs3732859	1.00[CEU][hapmap]
rs55780632	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56413771	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58032452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58188983	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6783750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72865746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72865751	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72865752	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72865754	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72865759	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73829287	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10490793	SH2D1A	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
6	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:42793600-42811000	Weak transcription	Lung	lung
8	chr3:42795600-42814000	Weak transcription	Gastric	stomach
9	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
10	chr3:42797600-42803800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42798600-42804000	Weak transcription	Stomach Mucosa	stomach
12	chr3:42798800-42803800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:42799000-42803400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:42801400-42803400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:42802200-42805000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:42802400-42803800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:42802400-42804600	Enhancers	Liver	Liver
19	chr3:42802400-42804600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:42802400-42804800	Enhancers	Adipose Nuclei	Adipose
21	chr3:42802400-42804800	Enhancers	NHDF-Ad	bronchial
22	chr3:42802400-42805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:42802400-42805000	Enhancers	HepG2	liver
24	chr3:42802400-42806400	Enhancers	Placenta	Placenta
25	chr3:42802600-42804000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:42802600-42804200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:42802600-42804600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:42802600-42804600	Enhancers	Brain Hippocampus Middle	brain
29	chr3:42802600-42805000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:42802600-42805000	Enhancers	Brain Anterior Caudate	brain
31	chr3:42802600-42805000	Enhancers	Osteobl	bone
32	chr3:42802600-42805400	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:42802600-42806200	Enhancers	Brain Substantia Nigra	brain
34	chr3:42802800-42803400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:42802800-42803400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:42802800-42803400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:42802800-42803400	Enhancers	Esophagus	oesophagus
38	chr3:42802800-42804400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:42802800-42804400	Weak transcription	A549	lung
40	chr3:42802800-42804600	Enhancers	Primary B cells from cord blood	blood
41	chr3:42802800-42804600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:42803000-42803400	Enhancers	Colonic Mucosa	Colon
43	chr3:42803000-42804400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:42803000-42804600	Enhancers	NHLF	lung
45	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
46	chr3:42803200-42804200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:42803200-42804400	Enhancers	Primary hematopoietic stem cells	blood
48	chr3:42803200-42806000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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