Variant report

Variant	rs13029968
Chromosome Location	chr2:38935110-38935111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12987870	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13006376	0.87[AMR][1000 genomes]
rs34429547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34460712	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558770	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35585199	0.81[EUR][1000 genomes]
rs74177081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv961401	chr2:38924660-38941942	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1800555	chr2:38929745-38950126	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1830359	chr2:38929745-38950126	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13029968	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 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	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
7	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
10	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:38913800-38938800	Weak transcription	Fetal Brain Male	brain
12	chr2:38914600-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:38914600-38938600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
15	chr2:38915800-38947200	Weak transcription	Ovary	ovary
16	chr2:38916800-38938800	Weak transcription	Fetal Lung	lung
17	chr2:38917200-38936400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
19	chr2:38918600-38947600	Weak transcription	Hela-S3	cervix
20	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:38918800-38937200	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:38920200-38942600	Weak transcription	Aorta	Aorta
23	chr2:38920400-38947800	Weak transcription	Esophagus	oesophagus
24	chr2:38921400-38947400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:38921600-38935800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:38921600-38938800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:38921600-38942800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:38924400-38936800	Weak transcription	Fetal Stomach	stomach
29	chr2:38924800-38936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:38927400-38947600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:38928200-38947800	Weak transcription	Stomach Mucosa	stomach
33	chr2:38928400-38936200	Weak transcription	Liver	Liver
34	chr2:38928600-38935800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
36	chr2:38929400-38937200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:38929800-38935800	Weak transcription	Primary T cells from cord blood	blood
38	chr2:38930000-38935800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:38930000-38937000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:38930000-38940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:38930000-38946800	Weak transcription	Right Atrium	heart
42	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:38930600-38938600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:38930600-38947000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:38930600-38965000	Weak transcription	Gastric	stomach
46	chr2:38930800-38943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:38931000-38943000	Weak transcription	NHLF	lung
48	chr2:38931000-38943200	Weak transcription	NHDF-Ad	bronchial
49	chr2:38931200-38948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:38931600-38937200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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