Variant report

Variant	rs6909857
Chromosome Location	chr6:142701158-142701159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142642858..142644453-chr6:142700060..142702054,2	MCF-7	breast:
2	chr6:142696462..142698436-chr6:142698561..142701397,2	MCF-7	breast:
3	chr6:142617568..142620556-chr6:142699575..142701431,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1040525	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040526	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1342060	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs1360194	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418201	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155259	0.86[EUR][1000 genomes]
rs1891308	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2039986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039987	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs2050157	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294764	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294771	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs262119	0.86[EUR][1000 genomes]
rs262121	0.86[EUR][1000 genomes]
rs262129	0.86[EUR][1000 genomes]
rs263178	0.84[EUR][1000 genomes]
rs263179	0.84[EUR][1000 genomes]
rs263180	0.86[EUR][1000 genomes]
rs263181	0.86[EUR][1000 genomes]
rs263182	0.86[EUR][1000 genomes]
rs263183	0.86[EUR][1000 genomes]
rs263184	0.86[EUR][1000 genomes]
rs263185	0.84[EUR][1000 genomes]
rs263186	0.86[EUR][1000 genomes]
rs263187	0.86[EUR][1000 genomes]
rs263188	0.86[EUR][1000 genomes]
rs263189	0.86[EUR][1000 genomes]
rs3748069	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817929	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896582	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs611802	0.82[EUR][1000 genomes]
rs6570507	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570508	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs6570509	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570510	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6929442	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6937121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741741	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753012	0.89[CEU][hapmap]
rs7754638	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7755109	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7756305	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs7763064	0.91[EUR][1000 genomes]
rs7770386	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7774095	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776375	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9373346	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389984	0.89[EUR][1000 genomes]
rs9389985	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389986	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389987	0.92[EUR][1000 genomes]
rs9399401	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9403380	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403381	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9403382	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403383	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403387	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9496346	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496369	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9496374	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9496392	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs962554	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs972982	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142697000-142703200	Weak transcription	NHDF-Ad	bronchial
2	chr6:142698000-142702000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:142698200-142702800	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:142698600-142706200	Weak transcription	NHLF	lung
5	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:142698800-142707600	Weak transcription	Placenta	Placenta
7	chr6:142698800-142707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:142699600-142702200	Genic enhancers	HepG2	liver
9	chr6:142699600-142708000	Weak transcription	Pancreas	Pancrea
10	chr6:142699600-142709200	Weak transcription	Fetal Intestine Large	intestine
11	chr6:142699800-142701400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:142699800-142702800	Weak transcription	HSMM	muscle
13	chr6:142699800-142705400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:142699800-142708000	Weak transcription	Liver	Liver
15	chr6:142699800-142709000	Weak transcription	Fetal Intestine Small	intestine
16	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:142700000-142701800	Enhancers	A549	lung
19	chr6:142700000-142703000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:142700000-142703000	Weak transcription	Osteobl	bone
21	chr6:142700000-142705600	Weak transcription	NHEK	skin
22	chr6:142700000-142705800	Weak transcription	NH-A	brain
23	chr6:142700000-142706000	Weak transcription	HSMMtube	muscle
24	chr6:142700000-142714200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:142700200-142701400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:142700200-142701400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:142700200-142701800	Weak transcription	HMEC	breast
28	chr6:142700200-142702200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:142700200-142705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:142700400-142701400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr6:142700400-142701400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:142700400-142702800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:142700400-142705600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:142700400-142709000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:142700400-142709000	Weak transcription	Fetal Lung	lung
36	chr6:142700600-142701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:142700600-142703000	Weak transcription	HUVEC	blood vessel
38	chr6:142700600-142705800	Weak transcription	Hela-S3	cervix
39	chr6:142700800-142701200	Weak transcription	Monocytes-CD14+_RO01746	blood

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