Variant report

Variant	rs13004674
Chromosome Location	chr2:38903865-38903866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38895186..38897690-chr2:38903114..38905637,2	K562	blood:
2	chr2:38902106..38905477-chr2:38907505..38910142,3	K562	blood:
3	chr2:38903554..38905525-chr2:38909598..38912564,2	MCF-7	breast:
4	chr2:38823625..38826319-chr2:38903588..38906507,3	K562	blood:
5	chr2:38893261..38895190-chr2:38902040..38904878,2	K562	blood:

Variant related genes	Relation type
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12469458	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12469534	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712612	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004806	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004842	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006376	0.95[EUR][1000 genomes]
rs13010022	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011383	0.86[ASN][1000 genomes]
rs13012704	0.90[EUR][1000 genomes]
rs13016907	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032255	0.88[ASN][1000 genomes]
rs13383762	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425086	0.82[ASN][1000 genomes]
rs17576472	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17576507	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28716236	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34391548	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34533539	0.93[ASN][1000 genomes]
rs34558770	0.87[EUR][1000 genomes]
rs34756536	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34875979	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34909144	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35448554	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35585199	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670885	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58757994	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707543	0.88[ASN][1000 genomes]
rs6736380	0.88[ASN][1000 genomes]
rs6741892	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13004674	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38904200	Weak transcription	Esophagus	oesophagus
2	chr2:38894000-38904400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:38894200-38904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:38894200-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:38894200-38904000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:38894200-38904600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:38894200-38906800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:38894400-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:38894400-38904000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:38894400-38904000	Weak transcription	Placenta	Placenta
13	chr2:38894400-38908600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:38894400-38910400	Weak transcription	Psoas Muscle	Psoas
15	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
16	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:38894600-38908000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
19	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:38895000-38917600	Weak transcription	HSMM	muscle
21	chr2:38895200-38908600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:38895600-38904400	Weak transcription	Stomach Mucosa	stomach
23	chr2:38895600-38904400	Weak transcription	Hela-S3	cervix
24	chr2:38895600-38906800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:38895600-38912400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:38895800-38904000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:38897800-38904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:38898000-38904400	Weak transcription	A549	lung
29	chr2:38898600-38904400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:38898600-38906800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:38898600-38908200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:38898600-38912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:38898800-38911600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:38900800-38904200	Weak transcription	Small Intestine	intestine
36	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
37	chr2:38901600-38906600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:38902000-38904000	Strong transcription	Fetal Intestine Small	intestine
39	chr2:38902200-38904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:38902400-38908800	Strong transcription	Primary T cells from cord blood	blood
41	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
42	chr2:38903000-38904000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:38903000-38904000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:38903000-38904000	Strong transcription	Liver	Liver
45	chr2:38903000-38904000	Strong transcription	Colonic Mucosa	Colon
46	chr2:38903000-38904000	Strong transcription	Fetal Intestine Large	intestine
47	chr2:38903000-38904000	Strong transcription	K562	blood
48	chr2:38903000-38904400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:38903000-38904400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:38903000-38904400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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