Variant report

Variant	rs9832489
Chromosome Location	chr3:105234988-105234989
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	chr3:105087236..105090040-chr3:105234697..105237400,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044243	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1157	1.00[YRI][hapmap]
rs13315085	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13315918	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13317140	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13317379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320956	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13322383	0.92[EUR][1000 genomes]
rs13325976	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17181561	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181701	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189101	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17189643	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17189711	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2291374	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28452673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772552	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72989914	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72989943	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73006164	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs751554	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7610031	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7619149	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7633779	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7645474	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9288807	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822014	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9825097	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9826369	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9828587	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9829190	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9830049	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9831077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839346	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9840990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841699	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9842772	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9842815	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9843750	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9847971	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9851399	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854028	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9855810	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9859198	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9859785	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9862725	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9866561	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870312	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9873424	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876895	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876906	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877002	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877483	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878315	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9882494	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990253	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
4	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
7	chr3:105225800-105236000	Weak transcription	Liver	Liver
8	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:105231000-105237400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:105232200-105245400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:105232200-105245400	Weak transcription	NHEK	skin
15	chr3:105232200-105245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
17	chr3:105232400-105237600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:105232400-105237600	Weak transcription	Fetal Heart	heart
19	chr3:105232600-105242400	Weak transcription	NHLF	lung
20	chr3:105232800-105236000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:105232800-105243200	Weak transcription	NH-A	brain
22	chr3:105233000-105235800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:105233000-105237800	Enhancers	A549	lung
24	chr3:105233200-105236000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:105233200-105237600	Weak transcription	NHDF-Ad	bronchial
26	chr3:105233200-105243200	Weak transcription	HMEC	breast
27	chr3:105233400-105237600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:105233400-105250600	Weak transcription	HSMM	muscle
29	chr3:105233600-105237400	Enhancers	Brain Hippocampus Middle	brain
30	chr3:105233800-105237800	Enhancers	Brain Substantia Nigra	brain
31	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:105234400-105236400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:105234600-105235600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:105234600-105235600	Weak transcription	Osteobl	bone
35	chr3:105234600-105236000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:105234600-105236200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:105234600-105236400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:105234600-105244000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:105234600-105244600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:105234800-105235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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