Variant report

Variant	rs2151131
Chromosome Location	chr9:103108941-103108942
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103108916..103110922-chr9:103189088..103192439,3	MCF-7	breast:
2	chr9:103108891..103111879-chr9:103188016..103191736,3	K562	blood:
3	chr9:103108889..103112022-chr9:103112659..103116565,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10118398	0.90[ASN][1000 genomes]
rs10118701	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10120244	0.88[ASN][1000 genomes]
rs10124133	0.90[ASN][1000 genomes]
rs10124893	0.81[ASN][1000 genomes]
rs10125785	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1014652	0.84[CHD][hapmap]
rs10819759	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs10819761	0.86[ASN][1000 genomes]
rs10819762	0.90[ASN][1000 genomes]
rs10819764	0.90[ASN][1000 genomes]
rs10819767	0.90[ASN][1000 genomes]
rs10989049	0.81[ASN][1000 genomes]
rs10989056	0.85[ASN][1000 genomes]
rs10989064	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs10989067	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs10989070	0.90[ASN][1000 genomes]
rs12684939	0.84[ASN][1000 genomes]
rs1338121	1.00[CHD][hapmap]
rs1338123	1.00[CHB][hapmap]
rs1338124	1.00[CHB][hapmap]
rs1338125	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1572607	0.84[CHD][hapmap]
rs1930243	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1930244	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961367	0.91[ASN][1000 genomes]
rs1999877	0.83[CHD][hapmap]
rs2026999	0.90[ASN][1000 genomes]
rs2065997	1.00[CHD][hapmap]
rs2210498	0.90[ASN][1000 genomes]
rs2245216	1.00[CHB][hapmap]
rs2417084	0.90[ASN][1000 genomes]
rs2417176	0.90[ASN][1000 genomes]
rs2476441	0.84[CHD][hapmap]
rs2485745	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2787364	0.83[CHD][hapmap]
rs2787365	0.84[CHD][hapmap]
rs2787368	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2787369	1.00[CHB][hapmap]
rs2787370	0.87[ASN][1000 genomes]
rs2787371	1.00[CHB][hapmap]
rs2787372	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs2787374	1.00[CHD][hapmap]
rs2787375	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2787376	0.89[ASN][1000 genomes]
rs2787377	0.81[ASN][1000 genomes]
rs2787380	1.00[CHB][hapmap]
rs2787390	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2787395	0.84[CHD][hapmap]
rs2787397	0.91[CHD][hapmap]
rs2806681	0.83[CHD][hapmap]
rs2806687	0.84[CHD][hapmap]
rs2806691	1.00[CHD][hapmap]
rs2806693	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2806694	1.00[CHB][hapmap]
rs2806695	1.00[CHB][hapmap]
rs2806696	1.00[CHB][hapmap]
rs2806699	1.00[CHD][hapmap]
rs2806700	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs2806702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2806703	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs28464821	0.86[ASN][1000 genomes]
rs3813712	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs3923501	0.81[ASN][1000 genomes]
rs4128230	0.85[ASN][1000 genomes]
rs4237194	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4237195	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs4237196	0.91[ASN][1000 genomes]
rs4446782	0.81[ASN][1000 genomes]
rs4742783	0.88[ASN][1000 genomes]
rs4742784	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs4743392	0.81[ASN][1000 genomes]
rs4743393	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs4743394	0.86[ASN][1000 genomes]
rs4743395	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs4743396	0.90[ASN][1000 genomes]
rs5029343	0.81[ASN][1000 genomes]
rs59242794	0.86[ASN][1000 genomes]
rs6479009	0.81[ASN][1000 genomes]
rs6479013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479014	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7020988	0.81[ASN][1000 genomes]
rs7021310	0.91[ASN][1000 genomes]
rs7025891	0.90[ASN][1000 genomes]
rs7025938	0.85[CHD][hapmap]
rs7035619	0.85[CHB][hapmap]
rs7036570	0.91[ASN][1000 genomes]
rs7047694	0.84[ASN][1000 genomes]
rs7048601	1.00[CHB][hapmap]
rs7849966	0.81[ASN][1000 genomes]
rs7852189	0.90[ASN][1000 genomes]
rs7860513	0.91[ASN][1000 genomes]
rs7864494	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7866850	0.91[ASN][1000 genomes]
rs7869985	0.91[ASN][1000 genomes]
rs7871702	0.91[ASN][1000 genomes]
rs7874900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs7875775	0.91[ASN][1000 genomes]
rs846753	0.84[CHD][hapmap]
rs846766	0.84[CHD][hapmap]
rs914711	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9299338	0.90[ASN][1000 genomes]
rs944710	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs946054	1.00[CHB][hapmap]
rs959893	0.88[ASN][1000 genomes]
rs9775182	0.81[ASN][1000 genomes]
rs9886877	0.84[CHD][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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2151131	TEX10	cis	parietal	SCAN
rs2151131	TEX10	cis	cerebellum	SCAN
rs2151131	MRPL50	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
2	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
4	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
5	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
7	chr9:103072200-103113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:103074000-103113200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:103078400-103111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:103078400-103112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:103078600-103109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:103082800-103111800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr9:103083800-103113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:103088400-103112000	Weak transcription	Brain Germinal Matrix	brain
15	chr9:103088600-103112400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:103088600-103113000	Weak transcription	Fetal Brain Female	brain
17	chr9:103088600-103114400	Weak transcription	Lung	lung
18	chr9:103088800-103112400	Weak transcription	Psoas Muscle	Psoas
19	chr9:103088800-103113400	Weak transcription	Fetal Intestine Small	intestine
20	chr9:103088800-103114400	Weak transcription	Gastric	stomach
21	chr9:103089400-103112800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:103090600-103111600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:103091000-103110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr9:103091200-103113200	Weak transcription	Liver	Liver
25	chr9:103092400-103112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:103092400-103113800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:103092600-103113800	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:103093400-103109000	Weak transcription	Ovary	ovary
29	chr9:103096000-103111000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:103099000-103111800	Strong transcription	K562	blood
31	chr9:103099800-103109800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr9:103100800-103109000	Weak transcription	Fetal Kidney	kidney
33	chr9:103100800-103109200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:103100800-103112600	Weak transcription	Aorta	Aorta
35	chr9:103100800-103113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:103101000-103111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:103101000-103113800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:103101400-103113200	Weak transcription	Fetal Stomach	stomach
39	chr9:103102000-103114000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:103103000-103109600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr9:103103200-103110400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:103103800-103110600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:103104400-103109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:103104400-103109000	Weak transcription	Thymus	Thymus
45	chr9:103104400-103109400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:103104600-103113800	Weak transcription	Right Ventricle	heart
47	chr9:103104800-103109000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:103104800-103111600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:103104800-103111600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:103104800-103112600	Weak transcription	Fetal Heart	heart

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