Variant report

Variant	rs16888222
Chromosome Location	chr6:56767158-56767159
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	chr6:56765319..56768240-chr6:56782219..56784389,2	K562	blood:
2	chr6:56766600..56772134-chr6:56817595..56821119,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10498814	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs11962430	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11963350	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451705	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451706	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1562908	0.82[JPT][hapmap]
rs17685218	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17685235	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903331	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2122958	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2397227	0.82[JPT][hapmap]
rs35301163	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818840	0.82[EUR][1000 genomes]
rs35942895	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58604217	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58721182	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59797084	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61273855	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411410	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62411427	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62411428	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411429	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459174	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925107	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6941401	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746010	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296855	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296856	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396250	0.82[JPT][hapmap]
rs9464405	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464407	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475744	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv1002581	chr6:56758291-56767820	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16888222	BEND6	cis	Esophagus Muscularis	GTEx
rs16888222	BEND6	cis	Artery Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56749200-56769600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:56753600-56769600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:56756000-56767400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:56756000-56769600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:56756000-56769600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:56756000-56770000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:56756200-56767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:56756200-56768400	Weak transcription	HMEC	breast
9	chr6:56756200-56768600	Weak transcription	HUVEC	blood vessel
10	chr6:56756200-56768800	Weak transcription	NHEK	skin
11	chr6:56756600-56775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:56756800-56771600	Weak transcription	K562	blood
13	chr6:56757200-56767400	Weak transcription	GM12878-XiMat	blood
14	chr6:56761000-56767400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:56763400-56767200	Weak transcription	Ovary	ovary
16	chr6:56763600-56769800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:56763800-56767200	Enhancers	HSMMtube	muscle
18	chr6:56763800-56774000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:56764000-56767400	Weak transcription	A549	lung
20	chr6:56764800-56771400	Weak transcription	NH-A	brain
21	chr6:56765000-56767200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:56765000-56767400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:56765000-56768000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:56765000-56771600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:56765200-56767200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:56765600-56768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:56765800-56770000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:56766000-56767200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:56766000-56767200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:56766000-56775800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:56766600-56767200	Enhancers	HSMM	muscle
32	chr6:56766600-56767600	Enhancers	Fetal Stomach	stomach
33	chr6:56766600-56768200	Enhancers	Osteobl	bone
34	chr6:56766800-56767200	Weak transcription	NHLF	lung
35	chr6:56766800-56767600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:56766800-56767600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:56766800-56767600	Enhancers	Brain Anterior Caudate	brain
38	chr6:56767000-56767200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:56767000-56767400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:56767000-56767400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:56767000-56767600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:56767000-56767600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr6:56767000-56768000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:56767000-56768200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:56767000-56768200	Enhancers	Cortex derived primary cultured neurospheres	brain

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