Variant report

Variant	rs16886402
Chromosome Location	chr6:75992041-75992042
allele	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	WRNIP1	chr6:75991837-75992097	GM12878	blood:	n/a	n/a
2	IRF1	chr6:75991918-75992098	K562	blood:	n/a	n/a
3	CHD1	chr6:75990856-75992049	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:75987095..75989976-chr6:75990032..75992457,3	MCF-7	breast:
2	chr6:75982220..75984333-chr6:75991304..75993082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225793	TF binding region
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16886319	1.00[EUR][1000 genomes]
rs16886374	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16886390	0.88[AFR][1000 genomes]
rs16886391	0.88[AFR][1000 genomes]
rs16886430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886450	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34148186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35227190	1.00[AMR][1000 genomes]
rs35449948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3756794	0.96[AFR][1000 genomes]
rs61025153	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75969600-75992200	Weak transcription	Colonic Mucosa	Colon
2	chr6:75970000-75992400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:75974200-75993000	Weak transcription	Placenta	Placenta
4	chr6:75975000-75992400	Weak transcription	Fetal Stomach	stomach
5	chr6:75978200-75992400	Weak transcription	Fetal Kidney	kidney
6	chr6:75978600-75993600	Weak transcription	Esophagus	oesophagus
7	chr6:75982600-75992400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:75982600-75993600	Weak transcription	Spleen	Spleen
9	chr6:75983000-75992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:75983000-75992400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:75983000-75992400	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:75983000-75992400	Weak transcription	Thymus	Thymus
13	chr6:75983000-75992600	Weak transcription	Fetal Thymus	thymus
14	chr6:75983000-75993200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:75983000-75993400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:75986400-75992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:75987400-75993600	Weak transcription	Lung	lung
18	chr6:75987600-75992400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:75987600-75992600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:75987800-75992400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:75987800-75996200	Active TSS	GM12878-XiMat	blood
22	chr6:75988000-75992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:75988000-75993000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:75988000-75993000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:75988000-75993200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:75988000-75993200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:75988200-75992200	Enhancers	Adipose Nuclei	Adipose
28	chr6:75988200-75992400	Enhancers	Fetal Brain Male	brain
29	chr6:75988200-75993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:75988400-75992400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:75988400-75992600	Enhancers	Primary T cells from cord blood	blood
32	chr6:75988800-75992400	Enhancers	Fetal Lung	lung
33	chr6:75988800-75992600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:75988800-75993400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:75988800-75993400	Weak transcription	Pancreas	Pancrea
36	chr6:75988800-75993600	Weak transcription	Gastric	stomach
37	chr6:75989000-75992400	Weak transcription	Left Ventricle	heart
38	chr6:75989200-75992400	Enhancers	Liver	Liver
39	chr6:75989200-75992400	Enhancers	Colon Smooth Muscle	Colon
40	chr6:75989200-75995800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:75989400-75992400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:75989400-75992400	Weak transcription	Right Ventricle	heart
43	chr6:75989400-75993400	Flanking Active TSS	HUVEC	blood vessel
44	chr6:75989400-75993800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:75989600-75992800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:75990000-75992200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:75990000-75992200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:75990000-75992400	Enhancers	Rectal Smooth Muscle	rectum
49	chr6:75990000-75995400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:75990200-75992200	Weak transcription	Brain Angular Gyrus	brain

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