Variant report

Variant	rs10779924
Chromosome Location	chr2:39208057-39208058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39207664..39211487-chr2:39212740..39218159,6	MCF-7	breast:
2	chr2:39201485..39204258-chr2:39207506..39209401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10153761	0.83[ASN][1000 genomes]
rs10166395	0.80[ASN][1000 genomes]
rs10166801	0.83[ASN][1000 genomes]
rs10172714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10183915	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10186762	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10192250	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10194374	0.83[ASN][1000 genomes]
rs10201980	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1037495	0.81[ASN][1000 genomes]
rs1043793	0.83[ASN][1000 genomes]
rs10439459	0.80[ASN][1000 genomes]
rs11124659	0.81[ASN][1000 genomes]
rs11692687	0.83[ASN][1000 genomes]
rs13023273	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454221	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1454222	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454223	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1454225	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454226	0.83[ASN][1000 genomes]
rs1454227	0.83[ASN][1000 genomes]
rs1454228	0.82[ASN][1000 genomes]
rs1470915	0.82[ASN][1000 genomes]
rs1531021	0.83[EUR][1000 genomes]
rs1840281	0.81[ASN][1000 genomes]
rs1869513	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869514	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1947432	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123881	0.82[ASN][1000 genomes]
rs2168044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278913	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278914	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290445	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305516	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2373474	0.81[ASN][1000 genomes]
rs2373495	0.83[ASN][1000 genomes]
rs2373496	0.83[ASN][1000 genomes]
rs2603145	0.83[EUR][1000 genomes]
rs2888585	0.82[ASN][1000 genomes]
rs371745	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3765058	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4142729	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs422854	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4643520	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670269	0.93[EUR][1000 genomes]
rs4670270	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670272	0.83[ASN][1000 genomes]
rs4670901	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670903	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670905	0.82[ASN][1000 genomes]
rs6544183	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6544184	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544185	1.00[EUR][1000 genomes]
rs6544187	0.86[AMR][1000 genomes]
rs6704656	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6713281	0.80[ASN][1000 genomes]
rs6716101	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725356	0.81[ASN][1000 genomes]
rs6725644	0.81[ASN][1000 genomes]
rs6752850	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6755527	0.86[AMR][1000 genomes]
rs6756184	0.83[ASN][1000 genomes]
rs7571052	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7573310	0.86[AMR][1000 genomes]
rs7577088	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7582918	0.83[EUR][1000 genomes]
rs7594644	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9309031	0.81[ASN][1000 genomes]
rs963731	0.92[ASN][1000 genomes]
rs9679498	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10779924	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39212400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:39188000-39212600	Weak transcription	Gastric	stomach
3	chr2:39188000-39213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39188200-39210800	Weak transcription	HMEC	breast
6	chr2:39188200-39211800	Weak transcription	Fetal Lung	lung
7	chr2:39188400-39212000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:39188400-39212400	Weak transcription	Fetal Brain Female	brain
9	chr2:39189200-39212000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39194000-39213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:39194600-39212000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:39194600-39212800	Weak transcription	Spleen	Spleen
14	chr2:39195200-39210400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:39195400-39212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:39196600-39212600	Weak transcription	Aorta	Aorta
17	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:39197200-39211000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:39197400-39210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:39198600-39212600	Weak transcription	HSMMtube	muscle
21	chr2:39198800-39212000	Weak transcription	Fetal Stomach	stomach
22	chr2:39199200-39211000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:39200000-39212000	Weak transcription	Primary T cells from cord blood	blood
25	chr2:39200000-39212200	Weak transcription	Pancreas	Pancrea
26	chr2:39200200-39212000	Weak transcription	Right Ventricle	heart
27	chr2:39200600-39210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
29	chr2:39201200-39210600	Weak transcription	HSMM	muscle
30	chr2:39201600-39211800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:39201600-39212800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:39201800-39212800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:39201800-39218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:39202000-39210400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:39202000-39211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:39202000-39212600	Weak transcription	Ovary	ovary
37	chr2:39202000-39218800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39202200-39210400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:39202200-39210800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:39202200-39212600	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:39202400-39210800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:39202800-39217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:39203600-39212000	Weak transcription	Lung	lung
47	chr2:39203800-39210200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:39204000-39210400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:39205000-39208600	Weak transcription	Primary B cells from cord blood	blood
50	chr2:39205200-39212800	Weak transcription	Left Ventricle	heart

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