Variant report

Variant	rs10439459
Chromosome Location	chr2:39236983-39236984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38977305..38979442-chr2:39235119..39237996,2	MCF-7	breast:
2	chr2:38978072..38979972-chr2:39235260..39237532,2	K562	blood:
3	chr2:39236974..39239611-chr2:39346618..39348424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10153761	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10165968	0.84[EUR][1000 genomes]
rs10166801	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10172085	0.94[EUR][1000 genomes]
rs10186762	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10190377	0.85[EUR][1000 genomes]
rs10192250	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10194374	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779924	0.80[ASN][1000 genomes]
rs11124659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124660	0.95[EUR][1000 genomes]
rs11692687	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12471731	0.80[ASN][1000 genomes]
rs12620003	0.84[EUR][1000 genomes]
rs12620071	0.96[EUR][1000 genomes]
rs12622969	0.82[EUR][1000 genomes]
rs12712630	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13023273	0.95[ASN][1000 genomes]
rs13031871	0.80[EUR][1000 genomes]
rs13033392	0.85[EUR][1000 genomes]
rs1377860	0.96[EUR][1000 genomes]
rs1377861	0.96[EUR][1000 genomes]
rs1377863	0.96[EUR][1000 genomes]
rs1454220	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1454221	0.85[ASN][1000 genomes]
rs1454222	0.84[ASN][1000 genomes]
rs1454223	0.94[ASN][1000 genomes]
rs1454225	0.95[ASN][1000 genomes]
rs1454226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1454227	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1454228	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1470914	0.84[EUR][1000 genomes]
rs1470915	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1840281	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947432	0.93[ASN][1000 genomes]
rs2060987	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2060989	0.96[EUR][1000 genomes]
rs2123876	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2123879	0.89[EUR][1000 genomes]
rs2123881	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2123882	0.83[EUR][1000 genomes]
rs2168042	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2278914	0.84[ASN][1000 genomes]
rs2290445	0.85[ASN][1000 genomes]
rs2373474	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2373495	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2373496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2888585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2924714	0.96[EUR][1000 genomes]
rs2969763	0.96[EUR][1000 genomes]
rs297121	0.96[EUR][1000 genomes]
rs297125	0.96[EUR][1000 genomes]
rs297128	0.96[EUR][1000 genomes]
rs297129	0.96[EUR][1000 genomes]
rs297130	0.96[EUR][1000 genomes]
rs297131	0.81[EUR][1000 genomes]
rs297132	0.82[EUR][1000 genomes]
rs297133	0.96[EUR][1000 genomes]
rs297134	0.82[EUR][1000 genomes]
rs297135	0.96[EUR][1000 genomes]
rs297136	0.82[EUR][1000 genomes]
rs297137	0.96[EUR][1000 genomes]
rs297139	0.96[EUR][1000 genomes]
rs297140	0.96[EUR][1000 genomes]
rs297141	0.96[EUR][1000 genomes]
rs297142	0.82[EUR][1000 genomes]
rs297143	0.96[EUR][1000 genomes]
rs297145	0.82[EUR][1000 genomes]
rs297147	0.82[EUR][1000 genomes]
rs297148	0.96[EUR][1000 genomes]
rs297149	0.96[EUR][1000 genomes]
rs297150	0.96[EUR][1000 genomes]
rs297151	0.84[EUR][1000 genomes]
rs297152	0.84[EUR][1000 genomes]
rs297153	0.96[EUR][1000 genomes]
rs297155	0.80[EUR][1000 genomes]
rs297156	0.84[EUR][1000 genomes]
rs297157	0.96[EUR][1000 genomes]
rs297158	0.95[EUR][1000 genomes]
rs297159	0.96[EUR][1000 genomes]
rs366840	0.82[EUR][1000 genomes]
rs378698	0.96[EUR][1000 genomes]
rs3796038	0.84[EUR][1000 genomes]
rs388958	0.82[EUR][1000 genomes]
rs4142729	0.94[ASN][1000 genomes]
rs4643520	0.95[ASN][1000 genomes]
rs4670270	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4670272	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670903	0.91[ASN][1000 genomes]
rs4670904	0.80[ASN][1000 genomes]
rs4670905	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670907	0.81[ASN][1000 genomes]
rs57378308	0.95[EUR][1000 genomes]
rs58645871	0.89[EUR][1000 genomes]
rs59732351	0.95[EUR][1000 genomes]
rs61405040	0.96[EUR][1000 genomes]
rs6419600	0.82[EUR][1000 genomes]
rs6544187	0.81[ASN][1000 genomes]
rs6544191	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6544194	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544195	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544197	0.96[EUR][1000 genomes]
rs6704656	0.80[ASN][1000 genomes]
rs6713281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6725356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6725644	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739568	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6752850	0.91[ASN][1000 genomes]
rs6756184	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72909662	0.95[EUR][1000 genomes]
rs7568552	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7573310	0.82[ASN][1000 genomes]
rs7577088	0.95[ASN][1000 genomes]
rs9309031	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963731	0.85[ASN][1000 genomes]
rs970409	0.96[EUR][1000 genomes]
rs997344	0.83[AMR][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	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
rs10439459	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
2	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
3	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
8	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
9	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
13	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
14	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
17	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:39219400-39242600	Weak transcription	Brain Substantia Nigra	brain
21	chr2:39220600-39237000	Strong transcription	Fetal Thymus	thymus
22	chr2:39221000-39241200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:39225400-39241800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:39225600-39241600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:39225600-39241600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:39225600-39241600	Strong transcription	Placenta	Placenta
27	chr2:39225800-39238000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:39225800-39241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:39226200-39241600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
31	chr2:39228000-39241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:39229000-39237200	Weak transcription	NH-A	brain
33	chr2:39229000-39251400	Weak transcription	Fetal Heart	heart
34	chr2:39229800-39239000	Weak transcription	K562	blood
35	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:39230200-39240000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:39230200-39243600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:39230400-39237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:39230600-39239000	Weak transcription	NHDF-Ad	bronchial
40	chr2:39230800-39237200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39231000-39239800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:39231200-39238800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:39231200-39241600	Strong transcription	HepG2	liver
44	chr2:39231600-39244400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:39231800-39241600	Strong transcription	Dnd41	blood
46	chr2:39232000-39237600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:39232000-39238000	Strong transcription	Fetal Lung	lung
48	chr2:39232000-39241200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:39232000-39241800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr2:39232200-39242800	Strong transcription	Liver	Liver

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