Variant report

Variant	rs9820656
Chromosome Location	chr3:99759816-99759817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99742093..99744324-chr3:99758867..99761377,2	MCF-7	breast:
2	chr3:99746722..99749482-chr3:99759616..99761759,2	MCF-7	breast:
3	chr3:99593477..99597773-chr3:99758944..99761226,4	K562	blood:
4	chr3:99590595..99595669-chr3:99758441..99761467,5	MCF-7	breast:
5	chr3:99757965..99760484-chr3:99766104..99767644,2	MCF-7	breast:
6	chr3:99720503..99722744-chr3:99759089..99760779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12330859	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs13326499	1.00[AFR][1000 genomes]
rs1387648	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs16841824	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs16841897	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs16841922	0.83[AFR][1000 genomes]
rs4434174	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs9819861	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9825938	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9826443	1.00[AFR][1000 genomes]
rs9829693	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9830284	1.00[AFR][1000 genomes]
rs9837440	1.00[AFR][1000 genomes]
rs9841296	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs9841678	1.00[AFR][1000 genomes]
rs9843812	1.00[AFR][1000 genomes]
rs9860687	1.00[AFR][1000 genomes]
rs9861168	0.83[AFR][1000 genomes]
rs9862384	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9870654	0.83[AFR][1000 genomes]
rs9871820	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs9883757	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs9990322	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
4	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
5	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:99751400-99761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:99752200-99774600	Weak transcription	Gastric	stomach
8	chr3:99753200-99761600	Weak transcription	Psoas Muscle	Psoas
9	chr3:99756000-99761400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:99757600-99762400	Enhancers	Fetal Intestine Large	intestine
11	chr3:99757800-99766800	Weak transcription	Pancreas	Pancrea
12	chr3:99758400-99760600	Enhancers	HUVEC	blood vessel
13	chr3:99758400-99760800	Enhancers	Fetal Lung	lung
14	chr3:99758400-99762600	Enhancers	NHLF	lung
15	chr3:99758600-99761600	Enhancers	HSMM	muscle
16	chr3:99758800-99760000	Enhancers	Primary B cells from cord blood	blood
17	chr3:99758800-99760000	Weak transcription	HepG2	liver
18	chr3:99758800-99760600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:99758800-99760800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:99758800-99761400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:99758800-99761400	Enhancers	NHDF-Ad	bronchial
22	chr3:99758800-99761400	Enhancers	Osteobl	bone
23	chr3:99758800-99762000	Enhancers	Fetal Stomach	stomach
24	chr3:99758800-99762000	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:99758800-99763800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:99759000-99760000	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:99759000-99760200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:99759000-99761800	Enhancers	Fetal Kidney	kidney
29	chr3:99759000-99762200	Enhancers	Colon Smooth Muscle	Colon
30	chr3:99759000-99762400	Enhancers	Rectal Smooth Muscle	rectum
31	chr3:99759000-99762800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:99759000-99762800	Enhancers	HMEC	breast
33	chr3:99759000-99763400	Enhancers	NHEK	skin
34	chr3:99759000-99766600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:99759200-99760200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:99759200-99760600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:99759200-99760600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:99759200-99760600	Enhancers	Hela-S3	cervix
39	chr3:99759200-99762000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:99759200-99762400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99759200-99762400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:99759200-99762600	Enhancers	NH-A	brain
43	chr3:99759200-99763200	Enhancers	Adipose Nuclei	Adipose
44	chr3:99759200-99766200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:99759200-99766400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:99759200-99768200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:99759400-99760000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr3:99759400-99760400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:99759400-99760800	Enhancers	Fetal Muscle Leg	muscle
50	chr3:99759400-99760800	Enhancers	Sigmoid Colon	Sigmoid Colon

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