Variant report

Variant	rs10183915
Chromosome Location	chr2:39218887-39218888
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39214682..39216969-chr2:39217834..39219459,2	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10166801	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10172714	0.85[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10186762	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10192250	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10194374	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10201980	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1043793	0.82[CHB][hapmap]
rs10779924	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12471731	0.90[CHB][hapmap]
rs12479098	1.00[AFR][1000 genomes]
rs12712630	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs13023273	0.81[EUR][1000 genomes]
rs1377860	0.85[CEU][hapmap];0.93[JPT][hapmap]
rs1454221	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1454222	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1454223	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1454225	0.83[EUR][1000 genomes]
rs1454226	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1470915	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1869513	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs1869514	0.82[EUR][1000 genomes]
rs1947432	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2060987	0.93[JPT][hapmap]
rs2060988	0.86[JPT][hapmap]
rs2123876	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2123879	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes]
rs2123881	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2168042	0.81[JPT][hapmap]
rs2168044	0.82[EUR][1000 genomes]
rs2278912	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278913	0.86[EUR][1000 genomes]
rs2278914	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2290445	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305516	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2373495	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2373496	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs2888585	0.85[CEU][hapmap]
rs297135	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs297148	1.00[CEU][hapmap]
rs297149	0.85[CEU][hapmap]
rs297150	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs297153	0.85[CEU][hapmap]
rs297158	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs297159	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs297160	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs368451	0.82[CEU][hapmap]
rs371745	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs372374	0.84[AMR][1000 genomes]
rs3765058	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs378698	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs4142729	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs422854	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs441869	0.80[AMR][1000 genomes]
rs4643520	0.81[EUR][1000 genomes]
rs4670269	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs4670270	0.81[EUR][1000 genomes]
rs4670272	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4670901	0.86[EUR][1000 genomes]
rs4670903	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58645871	1.00[AFR][1000 genomes]
rs6544183	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6544184	0.86[EUR][1000 genomes]
rs6544185	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6544187	0.83[ASN][1000 genomes]
rs6544191	0.85[ASN][1000 genomes]
rs6544197	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs6704656	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713281	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6716101	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs6725356	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6739568	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs6752850	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6756184	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7568552	0.86[ASN][1000 genomes]
rs7571052	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs7573310	0.91[ASN][1000 genomes]
rs7577088	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7594644	0.82[EUR][1000 genomes]
rs963730	0.91[CHB][hapmap]
rs963731	0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9679498	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997344	0.82[CHB][hapmap];0.87[JPT][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	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
rs10183915	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	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
4	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
5	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
9	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:39207600-39224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:39209200-39222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:39209200-39224000	Strong transcription	Placenta	Placenta
13	chr2:39209800-39224400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:39210400-39224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
18	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:39210800-39219200	Strong transcription	Fetal Thymus	thymus
22	chr2:39210800-39224800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:39210800-39230200	Strong transcription	Dnd41	blood
24	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39211200-39224800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:39211200-39228600	Strong transcription	HepG2	liver
27	chr2:39211400-39221200	Weak transcription	NHDF-Ad	bronchial
28	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
30	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
32	chr2:39213200-39221400	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:39213200-39221800	Weak transcription	HMEC	breast
34	chr2:39213400-39219200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:39213400-39219400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:39213400-39220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:39213400-39220400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:39213400-39220800	Weak transcription	Fetal Kidney	kidney
39	chr2:39213400-39221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:39213400-39221200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:39213400-39222200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:39213400-39223200	Weak transcription	GM12878-XiMat	blood
43	chr2:39213400-39224000	Weak transcription	NHLF	lung
44	chr2:39213400-39225600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:39213400-39225600	Weak transcription	Brain Anterior Caudate	brain
46	chr2:39213400-39225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:39213400-39225800	Weak transcription	Fetal Brain Female	brain
48	chr2:39213400-39225800	Weak transcription	Spleen	Spleen
49	chr2:39213400-39226400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:39213400-39226800	Weak transcription	Aorta	Aorta

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