Variant report

Variant	rs10988944
Chromosome Location	chr9:102774215-102774216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102765208..102767665-chr9:102771829..102774715,3	MCF-7	breast:
2	chr9:102769641..102771864-chr9:102771947..102774491,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10117638	0.82[YRI][hapmap]
rs10512269	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs1055187	0.86[YRI][hapmap]
rs10739792	0.82[YRI][hapmap]
rs10760707	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760708	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760719	1.00[CEU][hapmap]
rs10819718	0.93[EUR][1000 genomes]
rs10819721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs10819726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10819727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs10819730	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10819731	1.00[CEU][hapmap]
rs10819732	1.00[CEU][hapmap]
rs10988932	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988936	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988948	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988952	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988954	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10988955	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988956	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988957	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988960	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988964	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988966	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988972	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988977	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[MKK][hapmap]
rs10988982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap]
rs10988984	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988988	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs10988993	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988994	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap]
rs10989003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap]
rs10989004	1.00[CEU][hapmap]
rs10989007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap]
rs10989010	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989013	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11515448	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	0.89[CEU][hapmap]
rs11998890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12377746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs1338120	1.00[CHB][hapmap]
rs1415927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs14297	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs57875316	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap]
rs6479006	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7020150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020780	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs7021923	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7022208	0.82[YRI][hapmap]
rs7022643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7023412	0.83[AMR][1000 genomes]
rs7025271	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7025412	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs7026341	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026529	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026567	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7028564	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7028939	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031081	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7041818	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7043946	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047193	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7047693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs7350268	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73505717	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850961	0.91[AMR][1000 genomes]
rs7853497	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7854689	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7857556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs7858045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap]
rs7860268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs7860660	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7862614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs7865483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7866669	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7866950	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7867803	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs7868446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap]
rs7870469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870701	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7872897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7873545	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10988944	CYLC2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102718000-102777600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:102729600-102826800	Weak transcription	HMEC	breast
3	chr9:102731000-102778200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:102757400-102790600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:102759600-102777000	Weak transcription	HUVEC	blood vessel
6	chr9:102760800-102783400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:102761000-102778200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:102762000-102790000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:102763400-102783400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:102764200-102783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:102765200-102777000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:102766200-102778200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr9:102766400-102783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:102766400-102784600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:102766400-102785400	Weak transcription	Fetal Brain Male	brain
16	chr9:102766400-102787000	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:102766400-102794800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:102766600-102787200	Weak transcription	Psoas Muscle	Psoas
19	chr9:102766800-102783400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:102766800-102784600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:102766800-102793000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:102767000-102778000	Weak transcription	Fetal Stomach	stomach
23	chr9:102767000-102778200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:102767000-102781400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:102767000-102783400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:102767000-102783400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:102767000-102783400	Weak transcription	NHEK	skin
28	chr9:102767000-102785200	Weak transcription	Brain Substantia Nigra	brain
29	chr9:102767000-102785400	Weak transcription	Brain Germinal Matrix	brain
30	chr9:102767000-102787800	Weak transcription	Right Ventricle	heart
31	chr9:102767000-102799400	Weak transcription	Spleen	Spleen
32	chr9:102767000-102820400	Weak transcription	Colonic Mucosa	Colon
33	chr9:102767200-102775200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:102767200-102776800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:102767200-102777000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr9:102767200-102784800	Weak transcription	A549	lung
37	chr9:102767200-102789800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:102767200-102821800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:102767600-102776400	Weak transcription	Thymus	Thymus
40	chr9:102767600-102776600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:102767600-102776600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:102767600-102776800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr9:102767600-102776800	Weak transcription	Fetal Thymus	thymus
44	chr9:102767600-102777000	Weak transcription	Fetal Lung	lung
45	chr9:102767600-102777000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:102767600-102778000	Weak transcription	Aorta	Aorta
47	chr9:102767600-102778000	Weak transcription	Esophagus	oesophagus
48	chr9:102767600-102781800	Weak transcription	HepG2	liver
49	chr9:102767600-102783400	Weak transcription	Lung	lung
50	chr9:102767600-102785800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links