Variant report

Variant	rs9864412
Chromosome Location	chr3:78711350-78711351
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	chr3:78709553..78712856-chr3:78714127..78716792,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10865570	0.96[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708898	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714414	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11927671	0.96[CEU][hapmap]
rs2043662	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2118067	0.84[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164549	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255164	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2608023	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2684377	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28429251	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681009	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769521	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6785152	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7619742	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7631285	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs967454	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9834909	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837496	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs984138	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842948	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9856624	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9875094	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
2	chr3:78656000-78718600	Weak transcription	Fetal Intestine Large	intestine
3	chr3:78667200-78751200	Weak transcription	Esophagus	oesophagus
4	chr3:78676800-78730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:78679200-78720800	Weak transcription	Aorta	Aorta
6	chr3:78679200-78733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:78679400-78730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:78679400-78736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:78680400-78717800	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:78680400-78723600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:78682800-78715000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:78682800-78720200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:78693400-78730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:78694200-78730600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:78694400-78713600	Weak transcription	Fetal Brain Male	brain
16	chr3:78694400-78718400	Weak transcription	Fetal Heart	heart
17	chr3:78694400-78733200	Weak transcription	Fetal Kidney	kidney
18	chr3:78696800-78719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:78697200-78715000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:78697400-78715000	Weak transcription	NHEK	skin
21	chr3:78697800-78715400	Weak transcription	NH-A	brain
22	chr3:78698400-78717000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:78702800-78730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:78703000-78717200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:78703200-78739200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:78705400-78723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:78706200-78715400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:78706200-78715400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:78706400-78713200	Weak transcription	Fetal Lung	lung
30	chr3:78706400-78715000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:78706400-78716800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:78706400-78723600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:78706400-78736200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:78706600-78715400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:78706600-78717000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:78706600-78735200	Weak transcription	Primary T cells from cord blood	blood
37	chr3:78706600-78736400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:78706800-78713600	Weak transcription	Fetal Brain Female	brain
39	chr3:78706800-78716800	Weak transcription	HepG2	liver
40	chr3:78707000-78712800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:78707000-78715000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:78707000-78717200	Weak transcription	Ovary	ovary
43	chr3:78707000-78735400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:78707800-78718800	Weak transcription	Fetal Thymus	thymus
45	chr3:78709600-78715600	Weak transcription	HSMM	muscle
46	chr3:78709800-78713800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:78710400-78716800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:78710600-78711800	Enhancers	Brain Germinal Matrix	brain
49	chr3:78710600-78716800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:78711000-78711400	Active TSS	Brain Anterior Caudate	brain

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