Variant report

Variant	rs6564864
Chromosome Location	chr16:81309670-81309671
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81207703..81209401-chr16:81309474..81311615,2	MCF-7	breast:
2	chr16:81307769..81309694-chr16:81327148..81329061,2	MCF-7	breast:
3	chr16:81309026..81314264-chr16:81320854..81325448,12	MCF-7	breast:
4	chr16:81308065..81311392-chr16:81404971..81409467,4	MCF-7	breast:
5	chr16:81306937..81314493-chr16:81345040..81354910,36	MCF-7	breast:
6	chr16:81307371..81310396-chr16:81356696..81360378,4	MCF-7	breast:
7	chr16:81297837..81303804-chr16:81307756..81314186,17	MCF-7	breast:
8	chr16:81305711..81315624-chr16:81344956..81353172,47	MCF-7	breast:
9	chr16:81173729..81176012-chr16:81309308..81311406,2	MCF-7	breast:
10	chr16:81307461..81311487-chr16:81391240..81393766,3	MCF-7	breast:
11	chr16:81298705..81303185-chr16:81306285..81312157,8	MCF-7	breast:
12	chr16:81309186..81310055-chr16:83980377..83981202,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261609	Chromatin interaction
ENSG00000166473	Chromatin interaction
ENSG00000260495	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11642457	0.86[JPT][hapmap];0.95[AMR][1000 genomes]
rs12599057	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12924058	0.89[ASN][1000 genomes]
rs4889298	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7192170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7500488	0.90[AMR][1000 genomes]
rs9925200	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
3	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription 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	49 gene(s)	inside rSNPs	diseases
4	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
5	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
6	nsv527288	chr16:81204188-81310947	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv2755860	chr16:81262516-81333568	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81284600-81324600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:81300200-81311000	Weak transcription	Brain Anterior Caudate	brain
3	chr16:81300400-81312200	Weak transcription	Right Atrium	heart
4	chr16:81300600-81310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:81300600-81310000	Weak transcription	Spleen	Spleen
6	chr16:81306800-81311200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr16:81306800-81311600	Enhancers	Duodenum Mucosa	Duodenum
8	chr16:81306800-81312000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr16:81306800-81312600	Enhancers	Stomach Mucosa	stomach
10	chr16:81307000-81311400	Enhancers	Fetal Intestine Small	intestine
11	chr16:81307000-81311600	Enhancers	Fetal Intestine Large	intestine
12	chr16:81307600-81313000	Enhancers	Placenta	Placenta
13	chr16:81307800-81311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:81308200-81310000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr16:81308400-81311000	Enhancers	Esophagus	oesophagus
16	chr16:81308600-81311600	Enhancers	Colonic Mucosa	Colon
17	chr16:81308600-81312800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:81308800-81311200	Weak transcription	Fetal Kidney	kidney
19	chr16:81308800-81311600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr16:81309000-81310000	Active TSS	Rectal Smooth Muscle	rectum
21	chr16:81309000-81311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:81309000-81312000	Weak transcription	Gastric	stomach
23	chr16:81309200-81345200	Weak transcription	Brain Hippocampus Middle	brain
24	chr16:81309600-81310000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links