Variant report

Variant	rs10947646
Chromosome Location	chr6:36881535-36881536
allele	A/G
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	chr6:36881502..36882020-chr6:36986068..36986734,2	MCF-7	breast:
2	chr6:36878376..36882517-chr6:36952548..36956029,4	MCF-7	breast:
3	chr6:36852227..36855110-chr6:36880168..36882396,2	K562	blood:
4	chr6:36874669..36878220-chr6:36879029..36882017,3	MCF-7	breast:
5	chr6:36880047..36886049-chr6:36952384..36956049,12	MCF-7	breast:
6	chr6:36879267..36882648-chr6:36885620..36888336,3	K562	blood:
7	chr6:36875559..36878627-chr6:36879795..36881810,3	K562	blood:
8	chr6:36841055..36843830-chr6:36880674..36884413,4	MCF-7	breast:
9	chr6:36853041..36855950-chr6:36880214..36882571,4	MCF-7	breast:
10	chr6:36838232..36840562-chr6:36879914..36882282,2	MCF-7	breast:
11	chr6:36841357..36843245-chr6:36878241..36882187,3	K562	blood:
12	chr6:36856213..36857757-chr6:36880453..36883073,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000137409	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10456445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456447	0.84[AMR][1000 genomes]
rs10456448	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947648	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11964396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12111266	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12111291	1.00[ASN][1000 genomes]
rs12191780	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193721	0.82[ASN][1000 genomes]
rs12195012	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211502	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12215873	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524018	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12524649	1.00[ASN][1000 genomes]
rs12525180	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529199	1.00[JPT][hapmap]
rs12529769	1.00[ASN][1000 genomes]
rs17374068	0.85[CHD][hapmap];0.86[GIH][hapmap]
rs17552561	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272192	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41408445	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs4348312	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4714013	1.00[YRI][hapmap]
rs4714022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55928881	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56240344	1.00[ASN][1000 genomes]
rs56302344	1.00[ASN][1000 genomes]
rs66474948	1.00[ASN][1000 genomes]
rs72846078	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7745555	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7762601	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10947646	LRFN2	cis	cerebellum	SCAN
rs10947646	C6orf89	cis	cerebellum	SCAN
rs10947646	C6orf89	cis	parietal	SCAN
rs10947646	PNPLA1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:36866800-36881600	Strong transcription	Fetal Intestine Large	intestine
7	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:36868600-36882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:36870600-36882000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:36870600-36882000	Weak transcription	Fetal Kidney	kidney
11	chr6:36870800-36889400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:36871000-36888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:36871200-36882000	Weak transcription	Hela-S3	cervix
14	chr6:36874000-36882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:36876000-36885000	Strong transcription	Fetal Stomach	stomach
16	chr6:36876200-36885800	Weak transcription	Psoas Muscle	Psoas
17	chr6:36876800-36884200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:36876800-36885000	Weak transcription	Ovary	ovary
19	chr6:36876800-36885200	Weak transcription	Fetal Heart	heart
20	chr6:36877000-36884400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:36877800-36896000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:36879400-36881600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:36879400-36881600	Genic enhancers	Brain Cingulate Gyrus	brain
24	chr6:36879400-36882000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:36879400-36882200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:36879400-36882400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:36879400-36882800	Enhancers	NHEK	skin
28	chr6:36879400-36883000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:36879400-36883200	Strong transcription	Fetal Muscle Leg	muscle
30	chr6:36879400-36883400	Strong transcription	Fetal Lung	lung
31	chr6:36879400-36884400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:36879400-36894000	Strong transcription	Fetal Brain Female	brain
33	chr6:36879600-36881600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:36879600-36883200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:36879600-36894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:36879600-36895400	Strong transcription	Brain Germinal Matrix	brain
37	chr6:36879800-36882000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:36879800-36882000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:36879800-36882200	Enhancers	NH-A	brain
40	chr6:36879800-36882400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:36879800-36882400	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr6:36879800-36882400	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr6:36879800-36882400	Enhancers	HMEC	breast
44	chr6:36879800-36882600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:36879800-36883200	Strong transcription	Colon Smooth Muscle	Colon
46	chr6:36879800-36884400	Strong transcription	Placenta	Placenta
47	chr6:36879800-36885000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:36879800-36885000	Strong transcription	Left Ventricle	heart
49	chr6:36879800-36885200	Strong transcription	Right Ventricle	heart
50	chr6:36879800-36885400	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links