Variant report

Variant	rs10960774
Chromosome Location	chr9:12739313-12739314
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	chr9:12737180..12738894-chr9:12739213..12741322,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10491742	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10491743	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491744	0.84[AMR][1000 genomes]
rs1063380	1.00[CHB][hapmap]
rs1074789	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10756395	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10756405	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756406	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10809826	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10809829	1.00[ASN][1000 genomes]
rs10809836	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960758	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10960759	0.84[AMR][1000 genomes]
rs10960760	0.84[AMR][1000 genomes]
rs10960761	1.00[ASN][1000 genomes]
rs10960762	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs10960764	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10960765	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960775	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10960779	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960781	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789751	0.84[AMR][1000 genomes]
rs11829	0.84[AMR][1000 genomes]
rs12115198	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12379024	0.84[AMR][1000 genomes]
rs12379260	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12552462	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326788	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326789	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326790	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326791	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326792	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326797	0.84[AMR][1000 genomes]
rs1326798	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13284445	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284453	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284467	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284898	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13288130	0.81[AMR][1000 genomes]
rs13288475	0.84[AMR][1000 genomes]
rs13288636	0.84[AMR][1000 genomes]
rs13288681	0.84[AMR][1000 genomes]
rs13289304	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13295868	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13302551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409626	0.83[AMR][1000 genomes]
rs1409629	0.84[AMR][1000 genomes]
rs1409630	0.84[AMR][1000 genomes]
rs1543587	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346161	1.00[CHB][hapmap]
rs2209269	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209271	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209277	1.00[CHB][hapmap]
rs2224863	1.00[CHB][hapmap]
rs2382361	0.84[AMR][1000 genomes]
rs2733830	1.00[CHB][hapmap]
rs2733831	1.00[CHB][hapmap]
rs2733832	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2733833	1.00[CHB][hapmap]
rs2733834	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2733836	1.00[CHB][hapmap]
rs2762458	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs2762460	1.00[ASN][1000 genomes]
rs2762461	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2762463	1.00[CHB][hapmap]
rs2762464	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2890965	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35666741	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741245	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7019226	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7021368	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023927	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025678	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025771	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025842	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025914	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025953	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028587	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030485	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035500	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036011	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039325	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044022	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7466623	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910	1.00[CHB][hapmap]
rs927868	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs927869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs958073	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv8420	chr9:12725200-12750151	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3693020	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv818690	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv516527	chr9:12738690-12748486	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12719200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:12737400-12739400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:12737600-12741000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:12737800-12739400	Enhancers	NHDF-Ad	bronchial
5	chr9:12737800-12741200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:12738600-12739600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:12738800-12739600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:12739000-12739400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:12739000-12739600	Enhancers	Osteobl	bone
10	chr9:12739000-12741200	Enhancers	HMEC	breast
11	chr9:12739200-12739400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:12739200-12739600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:12739200-12739600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:12739200-12739600	Enhancers	Fetal Intestine Small	intestine
15	chr9:12739200-12740200	Weak transcription	Fetal Lung	lung
16	chr9:12739200-12741000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr9:12739200-12741400	Enhancers	NHEK	skin

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