Variant report

Variant	rs10124893
Chromosome Location	chr9:103065265-103065266
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	chr9:103062847..103065404-chr9:103075501..103077702,2	MCF-7	breast:

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10117799	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10118398	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10118701	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10120244	0.87[ASN][1000 genomes]
rs10123866	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123913	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10124133	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10125785	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10739796	0.85[JPT][hapmap]
rs10760724	0.93[ASN][1000 genomes]
rs10819751	0.93[ASN][1000 genomes]
rs10819756	0.81[ASN][1000 genomes]
rs10819759	0.88[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10819761	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10819762	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819764	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819767	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10988973	0.85[JPT][hapmap]
rs10989049	0.97[ASN][1000 genomes]
rs10989056	0.87[ASN][1000 genomes]
rs10989064	0.88[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10989067	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10989070	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11789196	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12336751	0.85[JPT][hapmap]
rs12552646	0.85[JPT][hapmap]
rs12684939	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1338121	0.84[ASN][1000 genomes]
rs1338123	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1338124	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1338125	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1338126	0.84[ASN][1000 genomes]
rs1415926	0.85[JPT][hapmap]
rs1535667	0.85[JPT][hapmap]
rs1930243	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1930244	0.81[ASN][1000 genomes]
rs1961367	0.87[ASN][1000 genomes]
rs2026999	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2057476	0.85[JPT][hapmap]
rs2065997	0.86[ASN][1000 genomes]
rs2151131	0.81[ASN][1000 genomes]
rs2210498	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245216	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2417084	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2417176	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476441	0.85[JPT][hapmap]
rs2485745	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2491098	0.82[ASN][1000 genomes]
rs2761056	0.85[JPT][hapmap]
rs2787363	0.85[JPT][hapmap]
rs2787364	0.85[JPT][hapmap]
rs2787365	0.85[JPT][hapmap]
rs2787368	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2787369	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2787370	0.90[ASN][1000 genomes]
rs2787371	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2787372	0.95[ASN][1000 genomes]
rs2787373	0.95[ASN][1000 genomes]
rs2787374	0.83[ASN][1000 genomes]
rs2787375	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2787376	0.91[ASN][1000 genomes]
rs2787377	0.97[ASN][1000 genomes]
rs2787379	0.85[ASN][1000 genomes]
rs2787380	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2787381	0.91[ASN][1000 genomes]
rs2787382	0.84[ASN][1000 genomes]
rs2787383	0.93[ASN][1000 genomes]
rs2787384	0.84[ASN][1000 genomes]
rs2787385	0.91[ASN][1000 genomes]
rs2787386	0.82[ASN][1000 genomes]
rs2787388	0.93[ASN][1000 genomes]
rs2787390	0.88[ASN][1000 genomes]
rs2787395	0.85[JPT][hapmap]
rs2787396	0.85[JPT][hapmap]
rs2787397	0.85[JPT][hapmap]
rs2806687	0.85[JPT][hapmap]
rs2806689	0.84[ASN][1000 genomes]
rs2806690	0.83[ASN][1000 genomes]
rs2806691	0.84[ASN][1000 genomes]
rs2806692	0.93[ASN][1000 genomes]
rs2806693	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2806694	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2806695	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2806696	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2806699	0.83[ASN][1000 genomes]
rs2806700	0.84[ASN][1000 genomes]
rs2806701	0.81[ASN][1000 genomes]
rs2806702	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2806703	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28464821	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813712	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3923501	0.97[ASN][1000 genomes]
rs4128230	0.93[ASN][1000 genomes]
rs4237194	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4237195	0.88[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237196	0.87[ASN][1000 genomes]
rs4446782	0.97[ASN][1000 genomes]
rs4742782	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742783	0.90[ASN][1000 genomes]
rs4742784	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743392	0.97[ASN][1000 genomes]
rs4743393	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743394	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743395	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743396	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5029342	0.82[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5029343	0.97[ASN][1000 genomes]
rs59242794	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479008	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479009	0.97[ASN][1000 genomes]
rs6479011	0.86[ASN][1000 genomes]
rs6479013	0.88[ASN][1000 genomes]
rs6479014	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7020988	0.97[ASN][1000 genomes]
rs7021310	0.87[ASN][1000 genomes]
rs7025891	0.85[ASN][1000 genomes]
rs7025938	0.93[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7035619	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7036570	0.87[ASN][1000 genomes]
rs7047694	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7048601	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7472	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7846794	0.85[JPT][hapmap]
rs7847213	0.85[JPT][hapmap]
rs7849966	0.97[ASN][1000 genomes]
rs7852189	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7854693	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860513	0.87[ASN][1000 genomes]
rs7861003	0.85[JPT][hapmap]
rs7864494	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs7866850	0.87[ASN][1000 genomes]
rs7869985	0.87[ASN][1000 genomes]
rs7871702	0.87[ASN][1000 genomes]
rs7874710	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7874900	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7875775	0.87[ASN][1000 genomes]
rs846752	0.85[JPT][hapmap]
rs846756	0.85[JPT][hapmap]
rs846759	0.85[JPT][hapmap]
rs846761	0.85[JPT][hapmap]
rs846766	0.85[JPT][hapmap]
rs846770	0.85[JPT][hapmap]
rs860171	0.85[JPT][hapmap]
rs914711	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9299338	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9408998	0.83[ASN][1000 genomes]
rs944710	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs946054	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs959893	0.90[ASN][1000 genomes]
rs9775014	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9775182	0.97[ASN][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	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
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10124893	TEX10	cis	Skin Sun Exposed Lower leg	GTEx
rs10124893	INVS	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044000-103067800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:103044200-103071200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
4	chr9:103044800-103067800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr9:103046000-103075400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr9:103046200-103072800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
9	chr9:103047400-103070800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:103048000-103068600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:103048000-103078000	Strong transcription	Primary T cells from cord blood	blood
12	chr9:103048200-103069600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:103048400-103068200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:103048400-103083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:103048600-103067600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:103049000-103073800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:103049400-103066800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr9:103049600-103065800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:103050000-103066400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:103050600-103067400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:103050600-103067400	Strong transcription	A549	lung
22	chr9:103050600-103069600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:103050600-103086400	Strong transcription	Dnd41	blood
24	chr9:103050800-103080400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:103051000-103068200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr9:103051000-103068400	Strong transcription	Fetal Muscle Leg	muscle
27	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:103051200-103066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:103051200-103067800	Strong transcription	Fetal Stomach	stomach
30	chr9:103051200-103078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:103051400-103068000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr9:103051400-103074000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:103051800-103066200	Strong transcription	Primary B cells from cord blood	blood
34	chr9:103052000-103067800	Strong transcription	Fetal Lung	lung
35	chr9:103052000-103068000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:103052600-103067400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:103052800-103066400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:103053000-103066400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr9:103053000-103066800	Strong transcription	NHLF	lung
40	chr9:103053000-103067800	Strong transcription	Thymus	Thymus
41	chr9:103053000-103068200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:103053000-103068400	Strong transcription	GM12878-XiMat	blood
43	chr9:103053200-103067000	Strong transcription	Placenta	Placenta
44	chr9:103053400-103067800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:103053400-103074800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:103054400-103066200	Strong transcription	Left Ventricle	heart
47	chr9:103054600-103069800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:103055800-103077600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
50	chr9:103057800-103066200	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links