Variant report

Variant	rs1869513
Chromosome Location	chr2:39205315-39205316
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	chr2:39204550..39206116-chr2:39208967..39211436,2	K562	blood:
2	chr2:39204062..39205776-chr2:39214858..39216979,2	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10153761	0.82[ASN][1000 genomes]
rs10165968	0.83[GIH][hapmap]
rs10166395	0.84[EUR][1000 genomes]
rs10166801	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10172714	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10177250	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs10183915	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs10186762	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192250	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10194374	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10201980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1037495	0.85[CHB][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1043793	1.00[CHB][hapmap];0.86[GIH][hapmap];0.82[ASN][1000 genomes]
rs10779924	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124659	0.80[ASN][1000 genomes]
rs11692687	0.82[ASN][1000 genomes]
rs12471731	0.92[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap]
rs12712630	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs13023273	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13031871	0.90[CHD][hapmap];0.86[GIH][hapmap]
rs1377860	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs1454221	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1454222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1454223	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454225	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1454226	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs1454227	0.82[ASN][1000 genomes]
rs1454228	0.81[ASN][1000 genomes]
rs1470915	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs1840281	0.80[ASN][1000 genomes]
rs1869514	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1947432	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060987	0.86[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs2060988	0.80[GIH][hapmap]
rs2123876	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2123879	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2123881	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2168042	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2168043	0.83[CHD][hapmap]
rs2168044	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278912	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278913	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278914	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290445	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373474	0.80[ASN][1000 genomes]
rs2373495	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2373496	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2888585	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs297120	0.83[GIH][hapmap]
rs297124	0.83[GIH][hapmap]
rs297135	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs297142	0.83[GIH][hapmap]
rs297148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs297149	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs297150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs297151	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs297152	0.87[CEU][hapmap]
rs297153	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs297158	0.87[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs297159	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs297160	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs371745	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3765058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs378698	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4142729	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs422854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4643520	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670269	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4670270	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670272	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs4670901	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670902	0.84[CHB][hapmap]
rs4670903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670905	0.81[ASN][1000 genomes]
rs6544183	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6544184	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6544185	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6544187	0.82[AMR][1000 genomes]
rs6544197	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6704656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6713281	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6716101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs672208	0.80[EUR][1000 genomes]
rs6725356	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs6725644	0.80[ASN][1000 genomes]
rs6739568	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs6752850	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755527	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6756184	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7571052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7573310	0.89[AMR][1000 genomes]
rs7577088	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7594644	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309031	0.80[ASN][1000 genomes]
rs958412	0.83[EUR][1000 genomes]
rs963730	0.91[CHB][hapmap]
rs963731	0.92[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9679498	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs997344	0.83[CHB][hapmap];0.85[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
rs1869513	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39212400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:39188000-39212600	Weak transcription	Gastric	stomach
3	chr2:39188000-39213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39188200-39210800	Weak transcription	HMEC	breast
6	chr2:39188200-39211800	Weak transcription	Fetal Lung	lung
7	chr2:39188400-39212000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:39188400-39212400	Weak transcription	Fetal Brain Female	brain
9	chr2:39189200-39212000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:39192000-39207400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:39194000-39213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39194400-39218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:39194600-39212000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:39194600-39212800	Weak transcription	Spleen	Spleen
15	chr2:39195200-39210400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:39195400-39212600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:39196600-39212600	Weak transcription	Aorta	Aorta
18	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:39197200-39211000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:39197400-39210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:39198600-39212600	Weak transcription	HSMMtube	muscle
22	chr2:39198800-39212000	Weak transcription	Fetal Stomach	stomach
23	chr2:39199200-39211000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:39199600-39220000	Weak transcription	Brain Germinal Matrix	brain
25	chr2:39200000-39212000	Weak transcription	Primary T cells from cord blood	blood
26	chr2:39200000-39212200	Weak transcription	Pancreas	Pancrea
27	chr2:39200200-39212000	Weak transcription	Right Ventricle	heart
28	chr2:39200600-39210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
30	chr2:39201200-39208000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:39201200-39210600	Weak transcription	HSMM	muscle
32	chr2:39201400-39205600	Weak transcription	Fetal Thymus	thymus
33	chr2:39201600-39211800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:39201600-39212800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:39201800-39212800	Weak transcription	Brain Angular Gyrus	brain
36	chr2:39201800-39218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:39202000-39205400	Weak transcription	Brain Anterior Caudate	brain
38	chr2:39202000-39205400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:39202000-39205600	Weak transcription	HepG2	liver
40	chr2:39202000-39205800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:39202000-39210400	Weak transcription	Adipose Nuclei	Adipose
42	chr2:39202000-39211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:39202000-39212600	Weak transcription	Ovary	ovary
44	chr2:39202000-39218800	Weak transcription	Brain Substantia Nigra	brain
45	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:39202200-39206800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:39202200-39210400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:39202200-39210800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:39202200-39212600	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:39202400-39210800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links