Variant report

Variant	rs12684841
Chromosome Location	chr9:97408971-97408972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97406984..97409530-chr9:97419873..97421419,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10993270	0.90[CHB][hapmap]
rs12006206	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs12685485	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16910850	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910853	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910860	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28369691	0.82[EUR][1000 genomes]
rs28402377	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402378	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402384	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402386	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402389	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402390	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28402396	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402397	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402401	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402404	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4111369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129219	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs59327242	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019207	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035325	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73523269	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73523271	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7849320	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850385	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867069	0.80[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap]

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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97402200-97410400	Weak transcription	Esophagus	oesophagus
2	chr9:97402400-97420000	Weak transcription	Right Atrium	heart
3	chr9:97402600-97411000	Weak transcription	Gastric	stomach
4	chr9:97402600-97415400	Weak transcription	Spleen	Spleen
5	chr9:97402800-97411600	Weak transcription	Primary B cells from cord blood	blood
6	chr9:97403000-97410600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:97405000-97410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97405200-97411200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:97405800-97410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:97405800-97418400	Weak transcription	Fetal Stomach	stomach
11	chr9:97406200-97410400	Weak transcription	Lung	lung
12	chr9:97406400-97410800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:97406800-97409000	Enhancers	Fetal Heart	heart
14	chr9:97407000-97410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:97407000-97410800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:97407000-97410800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:97407000-97411600	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:97407000-97411800	Weak transcription	Placenta	Placenta
19	chr9:97407200-97410000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:97407200-97410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:97407200-97410200	Weak transcription	Hela-S3	cervix
22	chr9:97407200-97410200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:97407200-97410400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr9:97407400-97410200	Weak transcription	HMEC	breast
25	chr9:97407400-97410400	Weak transcription	NHEK	skin
26	chr9:97407600-97410800	Weak transcription	HSMM	muscle
27	chr9:97408000-97409000	Enhancers	Stomach Mucosa	stomach
28	chr9:97408400-97411000	Weak transcription	HSMMtube	muscle
29	chr9:97408600-97410800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:97408800-97411600	Weak transcription	Fetal Intestine Small	intestine

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