Variant report

Variant	rs4928149
Chromosome Location	chr3:99685686-99685687
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99683941..99686099-chr3:99690442..99692720,2	MCF-7	breast:
2	chr3:99592456..99594885-chr3:99685238..99688172,2	MCF-7	breast:
3	chr3:99683725..99685720-chr3:99687425..99689237,2	MCF-7	breast:
4	chr3:99684840..99686543-chr3:99978018..99980934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10049383	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1017968	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs1021103	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10212525	0.86[ASW][hapmap];0.93[CEU][hapmap];0.82[GIH][hapmap]
rs1021341	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs1038294	1.00[ASW][hapmap];0.87[CEU][hapmap];0.80[GIH][hapmap];0.83[MKK][hapmap]
rs10511177	0.87[CEU][hapmap]
rs13064704	0.93[CEU][hapmap]
rs13069311	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs13093838	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13323143	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs1489816	0.86[ASW][hapmap];0.93[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs1688766	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.88[MKK][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1688771	0.93[CEU][hapmap]
rs17392948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34996634	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35154249	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4075038	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4361315	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap]
rs4571265	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap]
rs6790535	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs6790877	1.00[CEU][hapmap]
rs6799379	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs6802422	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap]
rs6806178	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs6807176	0.82[CEU][hapmap];0.80[GIH][hapmap]
rs704582	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.83[MKK][hapmap];0.81[EUR][1000 genomes]
rs7610486	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs7616988	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs7620228	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs7627991	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs793492	0.86[CEU][hapmap]
rs793496	1.00[ASW][hapmap];0.93[CEU][hapmap];0.80[GIH][hapmap]
rs793499	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes]
rs923470	0.93[CEU][hapmap]
rs923471	0.86[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap]
rs9289985	0.86[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]
rs9814359	0.87[CEU][hapmap]
rs9815439	0.87[CEU][hapmap]
rs9823908	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs9828079	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs9833888	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs9833980	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs9837602	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs9841186	1.00[ASW][hapmap];0.93[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs9851645	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs9854260	0.93[CEU][hapmap];0.92[GIH][hapmap]
rs9860290	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap]
rs9864437	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs9873709	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs9873878	0.93[CEU][hapmap]
rs9875640	0.87[CEU][hapmap]
rs9875878	0.86[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]

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	esv3325883	chr3:99684162-99687960	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
5	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:99679600-99688200	Weak transcription	GM12878-XiMat	blood
7	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:99681000-99685800	Weak transcription	Fetal Heart	heart
9	chr3:99683000-99687200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:99683200-99685800	Enhancers	Left Ventricle	heart
11	chr3:99683200-99686000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:99683200-99686400	Enhancers	Fetal Intestine Small	intestine
13	chr3:99683400-99687000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:99683400-99687200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:99683600-99688600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:99684200-99685800	Enhancers	Ovary	ovary
17	chr3:99684200-99686000	Enhancers	Small Intestine	intestine
18	chr3:99684200-99687400	Enhancers	HSMMtube	muscle
19	chr3:99684200-99688600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:99684200-99688800	Enhancers	NHEK	skin
21	chr3:99684400-99685800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:99684400-99685800	Enhancers	Pancreas	Pancrea
23	chr3:99684400-99686400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:99684400-99686400	Enhancers	Fetal Stomach	stomach
25	chr3:99684400-99688600	Enhancers	Psoas Muscle	Psoas
26	chr3:99684600-99685800	Weak transcription	HSMM	muscle
27	chr3:99684600-99686400	Enhancers	Colon Smooth Muscle	Colon
28	chr3:99684800-99685800	Weak transcription	Osteobl	bone
29	chr3:99684800-99686600	Enhancers	Fetal Muscle Leg	muscle
30	chr3:99685000-99686000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:99685000-99686200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:99685000-99687000	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:99685200-99686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:99685400-99685800	Weak transcription	HMEC	breast
35	chr3:99685400-99686400	Weak transcription	Aorta	Aorta
36	chr3:99685400-99687000	Enhancers	Stomach Mucosa	stomach
37	chr3:99685400-99687200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:99685400-99691400	Weak transcription	Right Atrium	heart
39	chr3:99685600-99685800	Enhancers	Gastric	stomach
40	chr3:99685600-99686000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:99685600-99686000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:99685600-99686000	Enhancers	Fetal Kidney	kidney
43	chr3:99685600-99686000	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr3:99685600-99686400	Enhancers	Adipose Nuclei	Adipose
45	chr3:99685600-99686600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:99685600-99688000	Enhancers	Placenta Amnion	Placenta Amnion

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