Variant report

Variant	rs3112164
Chromosome Location	chr2:39087890-39087891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39086851..39091387-chr2:39094171..39096771,4	K562	blood:

Variant related genes	Relation type
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10165289	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10186448	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10186842	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs10495883	1.00[GIH][hapmap]
rs12329307	1.00[EUR][1000 genomes]
rs13382974	1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13396461	1.00[EUR][1000 genomes]
rs13399254	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13407659	1.00[EUR][1000 genomes]
rs13409776	1.00[EUR][1000 genomes]
rs13420732	1.00[EUR][1000 genomes]
rs13421894	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1376461	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1451278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023037	1.00[EUR][1000 genomes]
rs17023042	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023045	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023214	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17023241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023292	1.00[EUR][1000 genomes]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28473018	1.00[EUR][1000 genomes]
rs28499207	1.00[EUR][1000 genomes]
rs3099938	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3099953	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099973	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112138	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112154	0.81[AFR][1000 genomes]
rs3112155	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[EUR][1000 genomes]
rs3112174	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112176	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112177	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322480	1.00[ASN][1000 genomes]
rs57884089	0.92[ASN][1000 genomes]
rs58412684	1.00[ASN][1000 genomes]
rs58645810	1.00[ASN][1000 genomes]
rs59788371	1.00[ASN][1000 genomes]
rs60406386	1.00[ASN][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61393528	1.00[ASN][1000 genomes]
rs6544182	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6712917	1.00[JPT][hapmap]
rs6722176	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6722478	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6748000	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs7368897	1.00[JPT][hapmap]
rs73930373	1.00[ASN][1000 genomes]
rs73930374	1.00[ASN][1000 genomes]
rs73930378	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7571935	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7605183	1.00[ASN][1000 genomes]
rs921433	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3112164	SOS1	cis	lymphoblastoid	seeQTL
rs3112164	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
2	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:39038800-39102200	Weak transcription	Gastric	stomach
4	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
5	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
7	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:39063600-39088400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:39067200-39090200	Weak transcription	Stomach Mucosa	stomach
10	chr2:39068400-39090600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:39072400-39089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:39072600-39090800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:39073000-39091200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:39073600-39090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:39075200-39090800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:39076000-39090600	Strong transcription	Brain Germinal Matrix	brain
18	chr2:39076200-39090600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:39076400-39090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:39076600-39090800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:39078000-39090800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:39078200-39091200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:39078400-39090600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:39078800-39090600	Strong transcription	Osteobl	bone
25	chr2:39079400-39090800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:39079600-39090400	Strong transcription	Fetal Thymus	thymus
27	chr2:39079600-39090800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr2:39079600-39090800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:39079600-39090800	Strong transcription	Fetal Brain Female	brain
30	chr2:39079800-39089600	Strong transcription	Fetal Stomach	stomach
31	chr2:39079800-39090600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:39079800-39090600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:39079800-39090600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:39079800-39090600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:39079800-39090600	Strong transcription	Brain Anterior Caudate	brain
36	chr2:39079800-39090600	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:39079800-39090600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:39079800-39090800	Strong transcription	Adipose Nuclei	Adipose
39	chr2:39079800-39091000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:39079800-39091000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:39079800-39091200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:39080000-39090800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:39080000-39090800	Strong transcription	Brain Hippocampus Middle	brain
44	chr2:39080000-39090800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:39080000-39092000	Strong transcription	Primary T cells from cord blood	blood
46	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:39080200-39089800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:39080200-39090200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:39081200-39088000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:39081200-39088200	Weak transcription	Small Intestine	intestine

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