Variant report

Variant	rs10989063
Chromosome Location	chr9:103108641-103108642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103106359..103108668-chr9:103193186..103195753,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10819755	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10819757	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10819758	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819760	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819765	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819766	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819768	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819771	0.91[CEU][hapmap]
rs10819772	0.91[CEU][hapmap]
rs10989041	0.91[EUR][1000 genomes]
rs10989046	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs10989047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989050	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989062	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989068	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989069	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989077	1.00[ASN][1000 genomes]
rs11515449	0.90[EUR][1000 genomes]
rs11515542	0.90[EUR][1000 genomes]
rs11788648	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790431	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs11791637	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11791943	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793726	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11795004	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000794	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs12002124	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs12003468	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs12005177	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352336	1.00[ASN][1000 genomes]
rs12375859	1.00[ASN][1000 genomes]
rs12379480	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284601	0.82[GIH][hapmap]
rs16919024	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs3199998	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274951	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274961	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579387	1.00[ASN][1000 genomes]
rs7028101	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036972	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037122	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037419	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039994	0.91[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs7849019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866700	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs7873560	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874036	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

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	chr9:103088800-103108800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:103088800-103112400	Weak transcription	Psoas Muscle	Psoas
20	chr9:103088800-103113400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:103088800-103114400	Weak transcription	Gastric	stomach
22	chr9:103089400-103112800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:103090600-103111600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:103091000-103110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr9:103091200-103113200	Weak transcription	Liver	Liver
26	chr9:103092400-103108800	Weak transcription	NHDF-Ad	bronchial
27	chr9:103092400-103112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:103092400-103113800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:103092600-103113800	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:103093400-103109000	Weak transcription	Ovary	ovary
31	chr9:103096000-103111000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:103099000-103111800	Strong transcription	K562	blood
33	chr9:103099800-103109800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr9:103100800-103109000	Weak transcription	Fetal Kidney	kidney
35	chr9:103100800-103109200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:103100800-103112600	Weak transcription	Aorta	Aorta
37	chr9:103100800-103113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:103101000-103111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:103101000-103113800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr9:103101400-103113200	Weak transcription	Fetal Stomach	stomach
41	chr9:103102000-103114000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:103103000-103109600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr9:103103200-103110400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:103103800-103110600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:103104400-103109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:103104400-103109000	Weak transcription	Thymus	Thymus
47	chr9:103104400-103109400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:103104600-103108800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:103104600-103108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:103104600-103108800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links