Variant report

Variant	rs2038686
Chromosome Location	chr9:95365219-95365220
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95363885..95366186-chr9:95423514..95426294,2	MCF-7	breast:
2	chr9:95364179..95365756-chr9:95368617..95371594,2	K562	blood:
3	chr9:95267270..95270140-chr9:95362878..95365869,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1010823	0.84[AMR][1000 genomes]
rs10820997	0.83[AMR][1000 genomes]
rs10821000	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10821002	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10821007	0.88[AMR][1000 genomes]
rs10821009	0.88[AMR][1000 genomes]
rs10821010	0.88[AMR][1000 genomes]
rs10821012	0.88[AMR][1000 genomes]
rs10821015	0.86[AMR][1000 genomes]
rs10821016	0.84[AMR][1000 genomes]
rs10992382	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992402	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992403	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992413	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992419	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992427	0.88[AMR][1000 genomes]
rs10992430	0.88[AMR][1000 genomes]
rs10992431	0.88[AMR][1000 genomes]
rs10992432	0.88[AMR][1000 genomes]
rs10992434	0.88[AMR][1000 genomes]
rs10992436	0.88[AMR][1000 genomes]
rs10992438	0.88[AMR][1000 genomes]
rs10992441	0.88[AMR][1000 genomes]
rs10992442	0.88[AMR][1000 genomes]
rs10992443	0.88[AMR][1000 genomes]
rs10992444	0.88[AMR][1000 genomes]
rs10992445	0.88[AMR][1000 genomes]
rs10992451	0.84[AMR][1000 genomes]
rs10992456	0.84[AMR][1000 genomes]
rs10992462	0.82[AMR][1000 genomes]
rs1117670	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1125063	0.84[AMR][1000 genomes]
rs1125064	0.84[AMR][1000 genomes]
rs12236393	0.88[AMR][1000 genomes]
rs12236516	0.86[AMR][1000 genomes]
rs12236747	0.86[AMR][1000 genomes]
rs12683944	0.88[AMR][1000 genomes]
rs12685256	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12685257	0.86[AMR][1000 genomes]
rs12685780	0.84[AMR][1000 genomes]
rs12685791	0.84[AMR][1000 genomes]
rs12686058	0.86[AMR][1000 genomes]
rs1326775	0.81[ASN][1000 genomes]
rs1552908	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980705	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2038685	0.82[ASN][1000 genomes]
rs2088055	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2181586	0.88[AMR][1000 genomes]
rs2274413	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277166	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2281888	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296080	0.88[AMR][1000 genomes]
rs3203916	0.88[AMR][1000 genomes]
rs41266683	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4545157	0.81[AMR][1000 genomes]
rs556	0.88[AMR][1000 genomes]
rs56111209	0.82[AMR][1000 genomes]
rs56203846	0.88[AMR][1000 genomes]
rs56339669	0.88[AMR][1000 genomes]
rs57421019	0.86[AMR][1000 genomes]
rs57720404	0.86[AMR][1000 genomes]
rs58045868	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60173654	0.88[AMR][1000 genomes]
rs60457563	0.82[AMR][1000 genomes]
rs6479426	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66493272	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs68022962	0.82[AMR][1000 genomes]
rs68046436	0.88[AMR][1000 genomes]
rs7037961	0.88[AMR][1000 genomes]
rs753802	0.88[AMR][1000 genomes]
rs753803	0.88[AMR][1000 genomes]
rs7863882	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7863890	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7864889	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7869529	0.88[AMR][1000 genomes]
rs7875227	0.88[AMR][1000 genomes]
rs8181065	0.88[AMR][1000 genomes]
rs878610	0.84[AMR][1000 genomes]
rs879812	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs912259	0.87[AMR][1000 genomes]
rs976320	0.88[AMR][1000 genomes]
rs976321	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038686	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95347600-95365800	Weak transcription	Thymus	Thymus
2	chr9:95355800-95367000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:95360200-95370200	Weak transcription	Fetal Heart	heart
4	chr9:95360400-95366000	Enhancers	Fetal Muscle Trunk	muscle
5	chr9:95360400-95366000	Enhancers	Fetal Muscle Leg	muscle
6	chr9:95361600-95366000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:95362200-95365600	Weak transcription	Dnd41	blood
8	chr9:95362800-95373000	Weak transcription	HMEC	breast
9	chr9:95363000-95370200	Weak transcription	Right Atrium	heart
10	chr9:95363000-95371400	Weak transcription	Right Ventricle	heart
11	chr9:95363200-95371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:95363400-95374000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:95363400-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:95364000-95366200	Weak transcription	NH-A	brain
15	chr9:95364000-95368600	Weak transcription	Osteobl	bone
16	chr9:95364000-95369400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:95364000-95370000	Weak transcription	Aorta	Aorta
18	chr9:95364000-95370400	Weak transcription	Ovary	ovary
19	chr9:95364000-95372800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:95364200-95365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:95364200-95365400	Weak transcription	Esophagus	oesophagus
22	chr9:95364200-95365600	Weak transcription	Pancreas	Pancrea
23	chr9:95364200-95365800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:95364400-95370200	Weak transcription	HSMMtube	muscle
25	chr9:95364400-95372800	Weak transcription	NHEK	skin
26	chr9:95364600-95368800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:95364800-95365800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:95364800-95370400	Weak transcription	Gastric	stomach
29	chr9:95365200-95366200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links