Variant report

Variant	rs16889055
Chromosome Location	chr6:36725726-36725727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:36725580-36725730	GM12873	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36560234..36563233-chr6:36722828..36725947,3	MCF-7	breast:
2	chr6:36725564..36727264-chr6:36727766..36730682,2	K562	blood:
3	chr6:36561839..36564756-chr6:36723772..36727529,4	MCF-7	breast:
4	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
5	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
6	chr6:36724390..36726745-chr6:36953555..36956553,2	K562	blood:

No data

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000112081	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11755091	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760163	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12055620	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12524933	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72856406	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs916296	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916298	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916299	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916300	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916301	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916302	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380592	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36709200-36727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:36718600-36725800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:36718600-36726600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:36718800-36726800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:36718800-36727400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:36718800-36727400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:36719600-36725800	Enhancers	HUVEC	blood vessel
8	chr6:36719600-36727000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:36719800-36726000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:36720000-36726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:36720200-36726400	Weak transcription	Pancreas	Pancrea
12	chr6:36720600-36726400	Weak transcription	HMEC	breast
13	chr6:36721200-36726600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:36721200-36726600	Weak transcription	Fetal Heart	heart
15	chr6:36721200-36726600	Weak transcription	HSMMtube	muscle
16	chr6:36721400-36726400	Weak transcription	Fetal Intestine Large	intestine
17	chr6:36721400-36726600	Weak transcription	Fetal Intestine Small	intestine
18	chr6:36721400-36728600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:36721800-36726600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:36721800-36726600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:36721800-36733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:36722600-36725800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:36722800-36727600	Enhancers	Stomach Mucosa	stomach
24	chr6:36722800-36748200	Weak transcription	Fetal Kidney	kidney
25	chr6:36723600-36726600	Enhancers	Placenta	Placenta
26	chr6:36723800-36726600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:36723800-36726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:36723800-36727400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:36723800-36736200	Weak transcription	Right Atrium	heart
30	chr6:36724000-36726600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:36724000-36728200	Weak transcription	Fetal Stomach	stomach
32	chr6:36724000-36736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:36724200-36726200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:36724200-36727200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:36724400-36726600	Weak transcription	A549	lung
36	chr6:36724400-36726800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:36724600-36726000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:36724800-36725800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:36724800-36726000	Enhancers	Colonic Mucosa	Colon
40	chr6:36724800-36726400	Weak transcription	Esophagus	oesophagus
41	chr6:36724800-36726400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:36724800-36726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:36724800-36727000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr6:36724800-36734400	Weak transcription	Right Ventricle	heart
45	chr6:36725000-36726600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:36725000-36726600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:36725000-36727400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:36725200-36726400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:36725200-36726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:36725200-36726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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