Variant report

Variant	rs16869301
Chromosome Location	chr6:71235647-71235648
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	chr6:71054941..71057178-chr6:71234683..71237663,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10080714	0.85[AFR][1000 genomes]
rs10440813	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10485117	0.86[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs12332812	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12332923	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869217	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869242	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869261	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2207424	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2223997	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28555262	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28885692	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3846749	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs747454	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9294867	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9294869	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9294870	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs9294873	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294875	1.00[AMR][1000 genomes]
rs9294877	0.82[AFR][1000 genomes]
rs9446243	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs9446244	0.89[YRI][hapmap]
rs9446247	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9446251	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446253	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446255	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446256	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446257	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446260	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446261	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446262	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446263	0.91[AFR][1000 genomes]
rs9446264	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446265	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446266	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446277	0.86[LWK][hapmap]
rs9455091	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9455096	0.91[YRI][hapmap]
rs9455102	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs9455103	0.91[YRI][hapmap]
rs9455107	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455109	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455110	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455112	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455115	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455116	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455117	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455118	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455119	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455120	0.86[ASW][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455122	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455123	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455124	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455126	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455127	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455128	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455131	0.86[ASW][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455134	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455135	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455136	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455137	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455141	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455142	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455143	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455145	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455147	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455148	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455152	1.00[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9455154	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455155	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455157	0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455159	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455175	0.80[AFR][1000 genomes]
rs9455183	0.82[AFR][1000 genomes]
rs9455184	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71210600-71262000	Weak transcription	Fetal Thymus	thymus
2	chr6:71214000-71236600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:71214000-71244800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:71214000-71248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:71214000-71248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:71214000-71249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:71214000-71250600	Weak transcription	Right Ventricle	heart
8	chr6:71214000-71253000	Weak transcription	Colonic Mucosa	Colon
9	chr6:71214000-71253000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:71214000-71256600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:71214000-71276000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:71214000-71276000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:71214000-71276000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:71214200-71248200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:71214400-71238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:71214400-71246000	Weak transcription	HMEC	breast
17	chr6:71214400-71251000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:71214400-71251800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:71214400-71257000	Weak transcription	Brain Anterior Caudate	brain
20	chr6:71214400-71262000	Weak transcription	Psoas Muscle	Psoas
21	chr6:71214600-71241600	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:71214600-71244000	Weak transcription	Esophagus	oesophagus
23	chr6:71214600-71244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:71214600-71248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:71214600-71248600	Weak transcription	NHEK	skin
26	chr6:71214600-71248800	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:71214600-71251200	Weak transcription	K562	blood
28	chr6:71214600-71276000	Weak transcription	A549	lung
29	chr6:71214800-71240400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:71215000-71273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:71216000-71240400	Weak transcription	GM12878-XiMat	blood
32	chr6:71216200-71262200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:71218000-71238600	Weak transcription	Stomach Mucosa	stomach
34	chr6:71219000-71258800	Weak transcription	Small Intestine	intestine
35	chr6:71225200-71236000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:71225200-71248800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:71226200-71244000	Weak transcription	Ovary	ovary
38	chr6:71228000-71248800	Weak transcription	Fetal Kidney	kidney
39	chr6:71228600-71276000	Weak transcription	Primary T cells from cord blood	blood
40	chr6:71229600-71276200	Weak transcription	Aorta	Aorta
41	chr6:71229800-71248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:71230400-71247400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:71231200-71268000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:71231800-71244200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:71231800-71257200	Weak transcription	Fetal Heart	heart
46	chr6:71232000-71241400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:71232200-71238400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:71232400-71237600	Strong transcription	Placenta	Placenta
49	chr6:71232800-71238600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:71232800-71251200	Weak transcription	H9 Cell Line	embryonic stem cell

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