Variant report

Variant	rs35585199
Chromosome Location	chr2:38923722-38923723
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38922245..38924157-chr2:38977097..38979272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12469458	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469534	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712612	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987870	0.85[EUR][1000 genomes]
rs13004674	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004806	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004842	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13005073	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13006376	0.91[EUR][1000 genomes]
rs13010022	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13011383	0.90[ASN][1000 genomes]
rs13012704	0.93[EUR][1000 genomes]
rs13016907	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029674	0.81[ASN][1000 genomes]
rs13029968	0.81[EUR][1000 genomes]
rs13032255	0.92[ASN][1000 genomes]
rs13383762	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13425086	0.86[ASN][1000 genomes]
rs17576472	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17576507	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28716236	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34391548	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34429547	0.83[EUR][1000 genomes]
rs34460712	0.81[EUR][1000 genomes]
rs34558770	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34756536	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34875979	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34909144	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35448554	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4670885	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58757994	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6707543	0.92[ASN][1000 genomes]
rs6736380	0.92[ASN][1000 genomes]
rs6741892	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74177081	0.81[EUR][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	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	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
rs35585199	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
8	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
9	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
12	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:38912600-38932000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:38912800-38924200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:38913800-38938800	Weak transcription	Fetal Brain Male	brain
16	chr2:38914400-38930000	Weak transcription	Left Ventricle	heart
17	chr2:38914600-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:38914600-38938600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
20	chr2:38915800-38947200	Weak transcription	Ovary	ovary
21	chr2:38916600-38932600	Weak transcription	Lung	lung
22	chr2:38916800-38938800	Weak transcription	Fetal Lung	lung
23	chr2:38917000-38927800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:38917200-38924600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:38917200-38936400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
27	chr2:38918600-38927400	Strong transcription	Fetal Intestine Small	intestine
28	chr2:38918600-38929600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:38918600-38947600	Weak transcription	Hela-S3	cervix
30	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:38918800-38929600	Weak transcription	HSMM	muscle
32	chr2:38918800-38937200	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:38919600-38924400	Strong transcription	Fetal Stomach	stomach
34	chr2:38919800-38927200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:38920200-38924400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:38920200-38928400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:38920200-38929000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:38920200-38942600	Weak transcription	Aorta	Aorta
39	chr2:38920400-38924200	Weak transcription	K562	blood
40	chr2:38920400-38926800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:38920400-38928800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:38920400-38947800	Weak transcription	Esophagus	oesophagus
43	chr2:38920600-38924600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:38920600-38934000	Weak transcription	Thymus	Thymus
45	chr2:38921000-38924200	Weak transcription	Fetal Thymus	thymus
46	chr2:38921000-38931800	Weak transcription	A549	lung
47	chr2:38921200-38924800	Weak transcription	Placenta	Placenta
48	chr2:38921200-38927200	Strong transcription	HepG2	liver
49	chr2:38921400-38924200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:38921400-38928000	Weak transcription	Stomach Mucosa	stomach

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