Variant report

Variant	rs9366707
Chromosome Location	chr6:27800502-27800503
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27799933-27802491	K562	blood:	n/a	n/a
2	POLR2A	chr6:27796592-27807059	K562	blood:	n/a	n/a
3	POLR2A	chr6:27799219-27808508	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26216002..26218813-chr6:27799737..27801689,2	MCF-7	breast:
2	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:
3	chr6:26197729..26199239-chr6:27800252..27802919,2	K562	blood:
4	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
5	chr6:26102897..26105879-chr6:27799887..27802546,2	MCF-7	breast:
6	chr6:26122973..26125036-chr6:27798042..27800567,2	MCF-7	breast:
7	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
8	chr6:27217724..27219322-chr6:27799079..27801494,2	MCF-7	breast:
9	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:
10	chr6:27798534..27801249-chrX:16803484..16805157,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H4K	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000086712	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16867983	0.80[ASN][1000 genomes]
rs1844435	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3175123	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34452669	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800321	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295751	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9348778	0.82[ASN][1000 genomes]
rs9348780	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366708	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380022	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380024	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393856	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27799000-27804200	Weak transcription	Spleen	Spleen
3	chr6:27799000-27804400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:27799000-27804600	Weak transcription	Lung	lung
5	chr6:27799000-27804600	Weak transcription	Ovary	ovary
6	chr6:27799000-27804600	Weak transcription	Pancreas	Pancrea
7	chr6:27799200-27801400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:27799200-27802200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:27799200-27802200	Weak transcription	A549	lung
10	chr6:27799200-27802800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:27799200-27802800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:27799200-27803000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:27799200-27804200	Weak transcription	Small Intestine	intestine
14	chr6:27799400-27804600	Weak transcription	Left Ventricle	heart
15	chr6:27799600-27800800	Weak transcription	HSMM	muscle
16	chr6:27799600-27802600	Weak transcription	Thymus	Thymus
17	chr6:27799600-27803800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:27799600-27803800	Weak transcription	Colonic Mucosa	Colon
19	chr6:27799600-27803800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:27799600-27803800	Weak transcription	Stomach Mucosa	stomach
21	chr6:27799600-27804000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:27799600-27804000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:27799600-27804000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:27799600-27804000	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:27799600-27804000	Weak transcription	Right Atrium	heart
26	chr6:27799600-27804200	Weak transcription	Right Ventricle	heart
27	chr6:27799800-27800600	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:27799800-27801200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:27799800-27801200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:27799800-27801200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:27799800-27801200	Weak transcription	Fetal Lung	lung
32	chr6:27799800-27801400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:27799800-27801400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:27799800-27802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:27799800-27802000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:27799800-27802000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:27799800-27802600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:27799800-27802600	Weak transcription	Fetal Intestine Large	intestine
39	chr6:27799800-27802600	Weak transcription	Fetal Kidney	kidney
40	chr6:27799800-27802600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:27799800-27802600	Weak transcription	NH-A	brain
42	chr6:27799800-27802800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:27799800-27802800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:27799800-27802800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:27799800-27802800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:27799800-27802800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:27799800-27802800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:27799800-27802800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:27799800-27802800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:27799800-27802800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links