Variant report

Variant	rs9834346
Chromosome Location	chr3:119753403-119753404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1037974	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13314836	0.95[AFR][1000 genomes]
rs13322562	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1579030	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17246730	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17246737	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903764	1.00[ASN][1000 genomes]
rs28821007	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002644	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3755556	1.00[JPT][hapmap]
rs4491944	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57027844	1.00[ASN][1000 genomes]
rs57132942	1.00[ASN][1000 genomes]
rs58299321	1.00[ASN][1000 genomes]
rs58371446	1.00[ASN][1000 genomes]
rs58991487	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59368677	1.00[ASN][1000 genomes]
rs59703574	0.86[ASN][1000 genomes]
rs60049973	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60325644	1.00[ASN][1000 genomes]
rs60993278	1.00[ASN][1000 genomes]
rs61091679	1.00[EUR][1000 genomes]
rs61188334	1.00[ASN][1000 genomes]
rs61511292	1.00[ASN][1000 genomes]
rs61566983	1.00[ASN][1000 genomes]
rs6796550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72548703	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854776	1.00[EUR][1000 genomes]
rs73854793	1.00[EUR][1000 genomes]
rs922337	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9812146	1.00[YRI][hapmap]
rs9812149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843795	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849889	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853463	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9865193	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9867915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9872321	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:119737400-119754000	Weak transcription	Small Intestine	intestine
3	chr3:119737800-119757200	Weak transcription	A549	lung
4	chr3:119739400-119756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119740000-119758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:119741000-119758000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:119741200-119758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:119741800-119753600	Weak transcription	Thymus	Thymus
9	chr3:119742000-119754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:119742000-119758000	Weak transcription	NHDF-Ad	bronchial
11	chr3:119742600-119757000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:119744200-119758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:119744400-119758400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119744800-119753600	Weak transcription	Fetal Thymus	thymus
15	chr3:119744800-119758000	Weak transcription	NHEK	skin
16	chr3:119745000-119757000	Weak transcription	Dnd41	blood
17	chr3:119745200-119758400	Weak transcription	HepG2	liver
18	chr3:119745400-119758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:119747400-119756200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:119747600-119758400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:119747800-119757000	Weak transcription	Lung	lung
22	chr3:119747800-119757200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:119747800-119757200	Weak transcription	Ovary	ovary
24	chr3:119747800-119758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:119748000-119758000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:119748400-119756400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:119748600-119755800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:119748800-119753600	Weak transcription	Left Ventricle	heart
29	chr3:119748800-119754600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:119748800-119756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:119748800-119757800	Weak transcription	Right Ventricle	heart
32	chr3:119749000-119758400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:119749200-119753600	Weak transcription	Psoas Muscle	Psoas
34	chr3:119749400-119755200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:119749600-119758000	Weak transcription	HSMM	muscle
36	chr3:119750200-119757000	Weak transcription	Esophagus	oesophagus
37	chr3:119750400-119754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:119750400-119758400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:119750600-119755200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:119750600-119757800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:119750600-119758000	Weak transcription	Fetal Lung	lung
42	chr3:119751800-119766800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:119752200-119757200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:119753000-119753600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:119753000-119753600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:119753000-119753800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:119753000-119754000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:119753200-119753600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:119753200-119757600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:119753400-119754800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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