Variant report

Variant	rs9849889
Chromosome Location	chr3:119603162-119603163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119593557..119595469-chr3:119602156..119604184,2	MCF-7	breast:
2	chr3:119539560..119540841-chr3:119602119..119603320,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1037974	1.00[JPT][hapmap]
rs13314836	0.93[AFR][1000 genomes]
rs13322562	0.87[AFR][1000 genomes]
rs1579030	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579032	1.00[ASN][1000 genomes]
rs17246730	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17246737	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28821007	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34002644	0.93[AFR][1000 genomes]
rs3732358	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4491944	1.00[JPT][hapmap]
rs57265162	1.00[ASN][1000 genomes]
rs58991487	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60049973	0.93[AFR][1000 genomes]
rs60675046	1.00[ASN][1000 genomes]
rs61091679	1.00[EUR][1000 genomes]
rs6796550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72548703	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73854776	1.00[EUR][1000 genomes]
rs922337	1.00[JPT][hapmap]
rs9812146	1.00[YRI][hapmap]
rs9812149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834346	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]
rs9843795	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853463	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865193	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9867915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9872321	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
3	chr3:119567000-119605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
5	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:119577600-119607600	Weak transcription	Aorta	Aorta
7	chr3:119577800-119607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119581800-119605400	Weak transcription	Colonic Mucosa	Colon
9	chr3:119582400-119607400	Weak transcription	Ovary	ovary
10	chr3:119582400-119607600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:119582400-119607600	Weak transcription	Fetal Brain Female	brain
12	chr3:119582400-119607600	Weak transcription	Thymus	Thymus
13	chr3:119582400-119607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
20	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
21	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
22	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:119582600-119607600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:119582600-119607800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:119582600-119609800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:119582600-119610600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:119582600-119611000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:119582600-119611000	Weak transcription	NHLF	lung
29	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
31	chr3:119582800-119607800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
33	chr3:119583000-119611000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:119583200-119603600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:119583600-119608000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:119583600-119621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:119584000-119622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:119585600-119607800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:119585800-119605600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:119590200-119605400	Weak transcription	GM12878-XiMat	blood
42	chr3:119592600-119617800	Weak transcription	Osteobl	bone
43	chr3:119593000-119605200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:119594000-119604400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:119594600-119603800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:119594600-119604800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:119594800-119610800	Weak transcription	Stomach Mucosa	stomach
48	chr3:119595800-119605600	Weak transcription	Fetal Lung	lung
49	chr3:119595800-119607600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:119595800-119607800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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