Variant report

Variant	rs3112160
Chromosome Location	chr2:39073321-39073322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39068375..39070499-chr2:39072460..39074648,2	K562	blood:
2	chr2:38977095..38979491-chr2:39071029..39074824,4	K562	blood:
3	chr2:39065545..39067577-chr2:39069948..39073607,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRSF7-3	chr2:39073209-39073418	expReg_chr2_2809_-

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

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]
rs10180775	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]
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]
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];0.92[ASN][1000 genomes]
rs1451278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023025	0.82[JPT][hapmap]
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]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];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]
rs3099953	1.00[EUR][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	1.00[EUR][1000 genomes]
rs3112138	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];0.82[LWK][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112176	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3112177	1.00[EUR][1000 genomes]
rs58412684	0.89[AMR][1000 genomes]
rs59473852	0.92[ASN][1000 genomes]
rs60406386	0.89[AMR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs6544182	1.00[JPT][hapmap]
rs6712917	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6722478	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6737680	1.00[EUR][1000 genomes]
rs6748000	1.00[JPT][hapmap]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6761115	0.92[ASN][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];0.92[ASN][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs921433	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap]

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	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
rs3112160	SOS1	cis	lymphoblastoid	seeQTL
rs3112160	SOS1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
4	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:39038800-39102200	Weak transcription	Gastric	stomach
6	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
8	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
10	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
11	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
12	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
14	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:39053800-39080200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:39053800-39080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:39054200-39076400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:39055000-39080000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:39055200-39085600	Weak transcription	Psoas Muscle	Psoas
20	chr2:39055600-39080000	Weak transcription	NH-A	brain
21	chr2:39055600-39080600	Weak transcription	Hela-S3	cervix
22	chr2:39055600-39080600	Weak transcription	K562	blood
23	chr2:39057000-39086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:39058000-39087800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:39060000-39080000	Weak transcription	Lung	lung
26	chr2:39060200-39075400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:39061200-39073400	Strong transcription	Fetal Intestine Large	intestine
28	chr2:39062400-39083400	Weak transcription	NHEK	skin
29	chr2:39063600-39079800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:39063600-39080600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:39063600-39088400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:39064000-39080000	Weak transcription	Fetal Brain Male	brain
33	chr2:39064200-39079800	Weak transcription	Thymus	Thymus
34	chr2:39064400-39081000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:39064600-39079800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:39065000-39076800	Weak transcription	GM12878-XiMat	blood
37	chr2:39065200-39080600	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:39065800-39079800	Weak transcription	Liver	Liver
39	chr2:39066000-39080000	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:39066800-39079800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:39067000-39078200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:39067200-39090200	Weak transcription	Stomach Mucosa	stomach
43	chr2:39067400-39076400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:39067600-39077600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:39067800-39073800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:39067800-39074600	Strong transcription	Brain Germinal Matrix	brain
47	chr2:39068000-39074600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:39068400-39074200	Strong transcription	Fetal Brain Female	brain
49	chr2:39068400-39074400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:39068400-39090600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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