Variant report

Variant	rs10484301
Chromosome Location	chr6:117842129-117842130
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	chr6:117802670..117804620-chr6:117839004..117842734,3	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10872154	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11153674	1.00[CHB][hapmap]
rs11751773	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12181630	1.00[ASW][hapmap]
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];0.97[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];0.94[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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72963492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965515	0.97[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[ASW][hapmap];1.00[CHB][hapmap]
rs9489143	1.00[CHB][hapmap]
rs9489242	1.00[ASW][hapmap]
rs9688605	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]
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
rs10484301	BRD7P3	cis	parietal	SCAN
rs10484301	ZUFSP	cis	parietal	SCAN
rs10484301	NT5DC1	cis	parietal	SCAN
rs10484301	BET3L	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	chr6:117819800-117868800	Weak transcription	Spleen	Spleen
3	chr6:117821600-117868800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:117821800-117843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:117823200-117868800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:117823200-117869600	Weak transcription	Small Intestine	intestine
7	chr6:117826200-117842600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:117826200-117844800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:117826400-117859800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:117827600-117851200	Weak transcription	Lung	lung
11	chr6:117828000-117866200	Weak transcription	Esophagus	oesophagus
12	chr6:117828200-117851000	Weak transcription	Right Atrium	heart
13	chr6:117828400-117851600	Weak transcription	NHLF	lung
14	chr6:117833600-117851600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:117833800-117847000	Weak transcription	NHEK	skin
16	chr6:117833800-117849200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:117834400-117852800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:117834400-117861800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:117834400-117863600	Weak transcription	Gastric	stomach
20	chr6:117834800-117846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:117834800-117851000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:117834800-117857400	Weak transcription	Aorta	Aorta
23	chr6:117834800-117860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:117835200-117851600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:117835200-117868800	Weak transcription	Colonic Mucosa	Colon
26	chr6:117835400-117868800	Weak transcription	Psoas Muscle	Psoas
27	chr6:117835600-117852600	Weak transcription	HSMMtube	muscle
28	chr6:117835800-117857600	Weak transcription	Placenta	Placenta
29	chr6:117836600-117861800	Weak transcription	Pancreas	Pancrea
30	chr6:117836600-117869600	Weak transcription	Stomach Mucosa	stomach
31	chr6:117837200-117860600	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:117838600-117849800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:117838600-117869000	Weak transcription	Ovary	ovary
34	chr6:117839000-117851400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:117840000-117842400	Genic enhancers	A549	lung
36	chr6:117840200-117842800	Strong transcription	NH-A	brain
37	chr6:117840600-117842600	Strong transcription	Osteobl	bone
38	chr6:117840800-117846200	Strong transcription	HMEC	breast
39	chr6:117841000-117842400	Strong transcription	Fetal Intestine Large	intestine
40	chr6:117841000-117844000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:117841000-117844400	Strong transcription	HepG2	liver
42	chr6:117841000-117845400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:117841000-117849000	Weak transcription	Liver	Liver
44	chr6:117841200-117848000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:117841400-117842200	Strong transcription	Left Ventricle	heart
46	chr6:117841400-117842800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr6:117841600-117842200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:117841600-117842200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:117841600-117842400	Strong transcription	Adipose Nuclei	Adipose
50	chr6:117841600-117842600	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links