Variant report

Variant	rs9688605
Chromosome Location	chr6:117831565-117831566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:117803526..117806489-chr6:117828214..117832875,5	MCF-7	breast:
2	chr6:117824091..117826926-chr6:117830247..117833617,3	MCF-7	breast:
3	chr6:117816660..117818857-chr6:117829332..117832262,2	MCF-7	breast:
4	chr6:117824027..117828169-chr6:117829590..117834365,6	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10484301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872154	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11153674	1.00[CHB][hapmap]
rs11751773	0.87[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192117	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12193035	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12197399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12200953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12205852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208894	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12210860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17637404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2134088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72963484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72963492	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965515	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745302	1.00[JPT][hapmap]
rs916305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs929059	1.00[JPT][hapmap]
rs9320605	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9481727	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9489124	1.00[CHB][hapmap]
rs9489143	1.00[CHB][hapmap]
rs9766117	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766945	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9767675	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9688605	BET3L	cis	parietal	SCAN
rs9688605	BRD7P3	cis	parietal	SCAN
rs9688605	NT5DC1	cis	parietal	SCAN
rs9688605	ZUFSP	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117805200-117851200	Weak transcription	Right Ventricle	heart
2	chr6:117816400-117841400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:117818400-117833600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:117819800-117831600	Weak transcription	Hela-S3	cervix
5	chr6:117819800-117834200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:117819800-117868800	Weak transcription	Spleen	Spleen
7	chr6:117821600-117868800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:117821800-117843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:117823200-117868800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:117823200-117869600	Weak transcription	Small Intestine	intestine
11	chr6:117825400-117833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:117826200-117842600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:117826200-117844800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:117826400-117859800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:117826600-117833400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:117827000-117834200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:117827200-117841600	Weak transcription	Adipose Nuclei	Adipose
18	chr6:117827600-117851200	Weak transcription	Lung	lung
19	chr6:117828000-117832000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:117828000-117833600	Weak transcription	Aorta	Aorta
21	chr6:117828000-117833600	Weak transcription	Gastric	stomach
22	chr6:117828000-117834400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:117828000-117834400	Weak transcription	Psoas Muscle	Psoas
24	chr6:117828000-117836400	Weak transcription	Liver	Liver
25	chr6:117828000-117841400	Weak transcription	Left Ventricle	heart
26	chr6:117828000-117866200	Weak transcription	Esophagus	oesophagus
27	chr6:117828200-117841000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:117828200-117851000	Weak transcription	Right Atrium	heart
29	chr6:117828400-117834400	Weak transcription	HSMMtube	muscle
30	chr6:117828400-117851600	Weak transcription	NHLF	lung
31	chr6:117828600-117833400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:117828600-117833800	Weak transcription	Fetal Kidney	kidney
33	chr6:117828800-117834000	Strong transcription	HSMM	muscle
34	chr6:117829000-117832000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr6:117829000-117832200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:117829000-117833000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:117829000-117833000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:117829000-117833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:117829000-117834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:117829400-117832000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:117829400-117832200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:117829600-117832200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:117829800-117831600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:117829800-117831600	Strong transcription	NH-A	brain
45	chr6:117830000-117832000	Weak transcription	HUVEC	blood vessel
46	chr6:117830400-117834200	Weak transcription	Fetal Lung	lung
47	chr6:117830400-117834400	Weak transcription	Pancreas	Pancrea
48	chr6:117830400-117834600	Weak transcription	Fetal Intestine Large	intestine
49	chr6:117830600-117831800	Strong transcription	HepG2	liver
50	chr6:117830800-117831600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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