Variant report

Variant	rs10190377
Chromosome Location	chr2:39250673-39250674
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	chr2:38977027..38978972-chr2:39249720..39251575,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10153761	0.85[EUR][1000 genomes]
rs10165968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10166395	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs10166631	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10166801	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10169337	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10172085	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10177250	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs10184015	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10194374	0.84[EUR][1000 genomes]
rs10200058	0.90[EUR][1000 genomes]
rs10204958	0.83[ASN][1000 genomes]
rs10205802	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10206751	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037495	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1043793	1.00[CEU][hapmap]
rs10439459	0.85[EUR][1000 genomes]
rs11124659	0.85[EUR][1000 genomes]
rs11124660	0.84[EUR][1000 genomes]
rs11674846	0.92[ASN][1000 genomes]
rs11691035	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12471731	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12620003	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs12620071	0.82[EUR][1000 genomes]
rs12622969	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs13031871	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13033392	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377860	0.82[EUR][1000 genomes]
rs1377861	0.82[EUR][1000 genomes]
rs1377863	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1377864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1454219	0.90[ASN][1000 genomes]
rs1454226	0.85[EUR][1000 genomes]
rs1454227	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1454228	0.81[EUR][1000 genomes]
rs1470914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1470915	0.85[EUR][1000 genomes]
rs1840281	0.81[EUR][1000 genomes]
rs1947433	0.87[ASN][1000 genomes]
rs2060988	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060989	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212322	0.82[EUR][1000 genomes]
rs2123876	0.82[EUR][1000 genomes]
rs2123881	0.85[EUR][1000 genomes]
rs2123882	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168042	0.86[CHB][hapmap]
rs2168043	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2373474	0.84[EUR][1000 genomes]
rs2373495	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2373496	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2373497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2888585	0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs2924714	0.82[EUR][1000 genomes]
rs2969763	0.82[EUR][1000 genomes]
rs297120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs297121	0.82[EUR][1000 genomes]
rs297124	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs297125	0.82[EUR][1000 genomes]
rs297127	0.91[EUR][1000 genomes]
rs297128	0.82[EUR][1000 genomes]
rs297129	0.82[EUR][1000 genomes]
rs297130	0.82[EUR][1000 genomes]
rs297131	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297132	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297133	0.82[EUR][1000 genomes]
rs297134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297135	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs297137	0.82[EUR][1000 genomes]
rs297139	0.82[EUR][1000 genomes]
rs297140	0.82[EUR][1000 genomes]
rs297141	0.82[EUR][1000 genomes]
rs297142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes]
rs297143	0.82[EUR][1000 genomes]
rs297144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs297145	0.94[EUR][1000 genomes]
rs297147	0.94[EUR][1000 genomes]
rs297148	0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs297149	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs297150	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297151	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs297152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs297153	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297155	0.91[EUR][1000 genomes]
rs297156	0.92[EUR][1000 genomes]
rs297157	0.82[EUR][1000 genomes]
rs297158	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs297159	0.82[EUR][1000 genomes]
rs297160	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs297161	0.91[EUR][1000 genomes]
rs366840	0.94[EUR][1000 genomes]
rs378698	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs3796038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs388958	0.94[EUR][1000 genomes]
rs4670269	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4670272	0.82[EUR][1000 genomes]
rs4670902	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4670904	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4670905	0.82[EUR][1000 genomes]
rs57378308	0.84[EUR][1000 genomes]
rs59732351	0.84[EUR][1000 genomes]
rs61405040	0.82[EUR][1000 genomes]
rs6419600	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6544186	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6544188	0.87[ASN][1000 genomes]
rs6544189	0.85[ASN][1000 genomes]
rs6544191	0.82[EUR][1000 genomes]
rs6544197	0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs6713281	0.85[EUR][1000 genomes]
rs6725356	0.84[EUR][1000 genomes]
rs6725644	0.84[EUR][1000 genomes]
rs6726833	0.87[EUR][1000 genomes]
rs6739807	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6756184	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6758330	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72909662	0.84[EUR][1000 genomes]
rs7568552	0.81[EUR][1000 genomes]
rs7582918	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7604229	0.91[ASN][1000 genomes]
rs7607509	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9309031	0.81[EUR][1000 genomes]
rs963730	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs970409	0.82[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10190377	SOS1	cis	multi-tissue	Pritchard
rs10190377	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	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
3	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
4	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
6	chr2:39229000-39251400	Weak transcription	Fetal Heart	heart
7	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:39235600-39251800	Weak transcription	NHEK	skin
11	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
13	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
14	chr2:39235600-39295800	Weak transcription	NHLF	lung
15	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
16	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
17	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
21	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
22	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:39236000-39305600	Weak transcription	Gastric	stomach
24	chr2:39236200-39305600	Weak transcription	Lung	lung
25	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
29	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
31	chr2:39239400-39254600	Weak transcription	Brain Germinal Matrix	brain
32	chr2:39240400-39250800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:39240800-39251400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:39240800-39257600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:39240800-39257800	Weak transcription	Fetal Brain Female	brain
36	chr2:39240800-39262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:39241000-39252000	Weak transcription	A549	lung
39	chr2:39241200-39256600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:39241200-39259800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
43	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
44	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:39244800-39257800	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:39245000-39251000	Active TSS	Right Atrium	heart
47	chr2:39246200-39251400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:39246200-39259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:39246400-39251400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:39246600-39250800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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