Variant report

Variant	rs16841897
Chromosome Location	chr3:99752477-99752478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

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]
rs13327351	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
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]
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]
rs9820656	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
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:53 , 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	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
5	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
6	chr3:99743800-99759200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:99744000-99753200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:99744200-99753000	Weak transcription	Fetal Kidney	kidney
9	chr3:99744200-99759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:99744400-99753000	Weak transcription	HepG2	liver
11	chr3:99746000-99758800	Weak transcription	Left Ventricle	heart
12	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:99748200-99753600	Enhancers	HSMM	muscle
14	chr3:99748600-99753800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:99748800-99753600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:99748800-99754000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:99749000-99753200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:99749000-99753600	Enhancers	HMEC	breast
19	chr3:99749000-99759400	Weak transcription	Stomach Mucosa	stomach
20	chr3:99749200-99753200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:99750400-99753600	Enhancers	NH-A	brain
22	chr3:99750400-99753600	Enhancers	Osteobl	bone
23	chr3:99750600-99757800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:99750800-99753200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:99750800-99753200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:99750800-99753800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:99751000-99752600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:99751000-99753200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:99751000-99753200	Enhancers	Psoas Muscle	Psoas
30	chr3:99751000-99753400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:99751000-99753600	Enhancers	Colon Smooth Muscle	Colon
32	chr3:99751000-99753800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr3:99751000-99759200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:99751200-99753200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:99751200-99753400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:99751200-99753400	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:99751200-99754000	Enhancers	Fetal Intestine Large	intestine
38	chr3:99751200-99754400	Enhancers	Fetal Intestine Small	intestine
39	chr3:99751400-99761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:99751600-99753400	Enhancers	NHDF-Ad	bronchial
41	chr3:99751800-99753200	Enhancers	Ovary	ovary
42	chr3:99751800-99755600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:99752000-99753000	Enhancers	HUVEC	blood vessel
44	chr3:99752000-99753200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:99752000-99753400	Enhancers	Fetal Stomach	stomach
46	chr3:99752000-99753800	Enhancers	HSMMtube	muscle
47	chr3:99752200-99752600	Enhancers	Fetal Lung	lung
48	chr3:99752200-99753800	Enhancers	A549	lung
49	chr3:99752200-99759400	Weak transcription	Small Intestine	intestine
50	chr3:99752200-99774600	Weak transcription	Gastric	stomach

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