Variant report

Variant	rs12493320
Chromosome Location	chr3:99750222-99750223
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12486901	1.00[CEU][hapmap]
rs12489030	1.00[CEU][hapmap]
rs12490054	1.00[CHB][hapmap]
rs12491153	1.00[AFR][1000 genomes]
rs12493124	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs3921767	1.00[CEU][hapmap]
rs4928152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874130	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs55881709	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140081	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs62281674	1.00[ASN][1000 genomes]
rs6792339	1.00[CEU][hapmap]
rs6800456	1.00[CEU][hapmap]
rs7632345	1.00[CEU][hapmap]
rs7635633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][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:47 , 50 per page) page: 1

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	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:99735600-99750400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
7	chr3:99742200-99751000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
9	chr3:99743000-99750800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:99743800-99751000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:99743800-99751200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:99743800-99752200	Weak transcription	A549	lung
13	chr3:99743800-99759200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:99744000-99753200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:99744200-99750800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:99744200-99753000	Weak transcription	Fetal Kidney	kidney
17	chr3:99744200-99759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:99744400-99753000	Weak transcription	HepG2	liver
19	chr3:99744600-99750400	Weak transcription	NH-A	brain
20	chr3:99744600-99750400	Weak transcription	Osteobl	bone
21	chr3:99744800-99751000	Weak transcription	NHDF-Ad	bronchial
22	chr3:99744800-99751200	Weak transcription	Ovary	ovary
23	chr3:99745200-99751800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:99746000-99758800	Weak transcription	Left Ventricle	heart
25	chr3:99746400-99751200	Weak transcription	Pancreas	Pancrea
26	chr3:99746600-99751000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:99746800-99750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:99746800-99752000	Weak transcription	HUVEC	blood vessel
30	chr3:99748200-99753600	Enhancers	HSMM	muscle
31	chr3:99748600-99751600	Enhancers	HSMMtube	muscle
32	chr3:99748600-99753800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:99748800-99751200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:99748800-99751200	Enhancers	NHEK	skin
35	chr3:99748800-99753600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:99748800-99754000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:99749000-99750600	Enhancers	Fetal Thymus	thymus
38	chr3:99749000-99751200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:99749000-99751600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:99749000-99753200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:99749000-99753600	Enhancers	HMEC	breast
42	chr3:99749000-99759400	Weak transcription	Stomach Mucosa	stomach
43	chr3:99749200-99753200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:99749600-99750600	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr3:99749600-99751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:99749600-99751200	Weak transcription	Fetal Intestine Large	intestine
47	chr3:99750200-99750800	Enhancers	Psoas Muscle	Psoas

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