Variant report

Variant	rs28885692
Chromosome Location	chr6:71220460-71220461
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:71220397-71220585	HepG2	liver:	n/a	chr6:71220493-71220508
2	MAFK	chr6:71220365-71220552	IMR90	lung:	n/a	chr6:71220493-71220508
3	BATF	chr6:71220410-71220567	GM12878	blood:	n/a	chr6:71220500-71220511
4	MAFK	chr6:71220407-71220607	H1-hESC	embryonic stem cell:	n/a	chr6:71220493-71220508
5	MAFK	chr6:71220373-71220648	HepG2	liver:	n/a	chr6:71220493-71220508

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71213174..71214836-chr6:71218767..71221029,2	K562	blood:

Variant related genes	Relation type
RNU7-48P	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10080714	0.84[AFR][1000 genomes]
rs10440813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10485117	0.91[AFR][1000 genomes]
rs12332812	0.84[AFR][1000 genomes]
rs12332923	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869261	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2207424	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2223997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28555262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3846749	0.91[AFR][1000 genomes]
rs747454	0.84[AFR][1000 genomes]
rs9294867	0.81[AFR][1000 genomes]
rs9294869	0.84[AFR][1000 genomes]
rs9294870	0.91[AFR][1000 genomes]
rs9294873	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294875	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294877	0.81[AFR][1000 genomes]
rs9446243	0.91[AFR][1000 genomes]
rs9446247	0.84[AFR][1000 genomes]
rs9446251	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446253	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446256	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446259	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446263	0.98[AFR][1000 genomes]
rs9446264	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446266	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455102	0.91[AFR][1000 genomes]
rs9455103	0.83[AFR][1000 genomes]
rs9455107	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455110	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455112	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455115	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455116	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455117	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455118	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455119	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455122	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455124	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455126	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455127	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455128	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455142	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455145	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455146	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455152	0.93[AFR][1000 genomes]
rs9455154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455159	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455183	0.81[AFR][1000 genomes]
rs9455184	0.81[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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71210600-71262000	Weak transcription	Fetal Thymus	thymus
2	chr6:71211400-71221600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:71214000-71220600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:71214000-71236600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:71214000-71244800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:71214000-71248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:71214000-71248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:71214000-71249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:71214000-71250600	Weak transcription	Right Ventricle	heart
10	chr6:71214000-71253000	Weak transcription	Colonic Mucosa	Colon
11	chr6:71214000-71253000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:71214000-71256600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:71214000-71276000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:71214000-71276000	Weak transcription	Brain Germinal Matrix	brain
15	chr6:71214000-71276000	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:71214200-71225800	Weak transcription	Ovary	ovary
17	chr6:71214200-71234000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:71214200-71234400	Weak transcription	Liver	Liver
19	chr6:71214200-71248200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:71214400-71224800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:71214400-71226200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:71214400-71226200	Weak transcription	Fetal Brain Male	brain
23	chr6:71214400-71234200	Weak transcription	HepG2	liver
24	chr6:71214400-71238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:71214400-71246000	Weak transcription	HMEC	breast
26	chr6:71214400-71251000	Weak transcription	Brain Substantia Nigra	brain
27	chr6:71214400-71251800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:71214400-71257000	Weak transcription	Brain Anterior Caudate	brain
29	chr6:71214400-71262000	Weak transcription	Psoas Muscle	Psoas
30	chr6:71214600-71221600	Weak transcription	Aorta	Aorta
31	chr6:71214600-71227800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:71214600-71234600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:71214600-71241600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:71214600-71244000	Weak transcription	Esophagus	oesophagus
35	chr6:71214600-71244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:71214600-71248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:71214600-71248600	Weak transcription	NHEK	skin
38	chr6:71214600-71248800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:71214600-71251200	Weak transcription	K562	blood
40	chr6:71214600-71276000	Weak transcription	A549	lung
41	chr6:71214800-71240400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:71215000-71226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:71215000-71273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:71215200-71224000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:71215200-71224000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:71215200-71224200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:71215200-71224200	Weak transcription	Adipose Nuclei	Adipose
48	chr6:71215200-71234600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:71216000-71232400	Weak transcription	Placenta	Placenta
50	chr6:71216000-71240400	Weak transcription	GM12878-XiMat	blood

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