Variant report

Variant	rs6769676
Chromosome Location	chr3:141461847-141461848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr3:141461810-141461873	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141460791..141464587-chr3:141594120..141597016,3	MCF-7	breast:
2	chr20:26189934..26190604-chr3:141461091..141462091,2	MCF-7	breast:
3	chr3:141460404..141464291-chr3:141593804..141597029,4	MCF-7	breast:

Variant related genes	Relation type
RNF7	TF binding region
ENSG00000227195	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1055690	0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs1980190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61270966	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440034	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000305	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635763	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs9789997	0.97[AMR][1000 genomes];1.00[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6769676	GRK7	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:141458400-141463600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:141458400-141464000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:141458600-141463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:141458600-141468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
7	chr3:141459000-141462000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:141459000-141462400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:141459000-141463200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:141459000-141463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:141459000-141463600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:141459000-141463600	Weak transcription	Esophagus	oesophagus
13	chr3:141459000-141465600	Weak transcription	Lung	lung
14	chr3:141459000-141465800	Weak transcription	Gastric	stomach
15	chr3:141459400-141464000	Weak transcription	Fetal Stomach	stomach
16	chr3:141459600-141463400	Weak transcription	Fetal Brain Female	brain
17	chr3:141459600-141464200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
19	chr3:141459800-141463400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:141460000-141463600	Weak transcription	Fetal Kidney	kidney
21	chr3:141460000-141467000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:141460200-141462000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:141460200-141462000	Weak transcription	Fetal Lung	lung
24	chr3:141460200-141462200	Weak transcription	Hela-S3	cervix
25	chr3:141460200-141463200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:141460200-141463400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:141460200-141463400	Weak transcription	Thymus	Thymus
28	chr3:141460200-141463400	Weak transcription	HMEC	breast
29	chr3:141460200-141463600	Weak transcription	Colonic Mucosa	Colon
30	chr3:141460200-141464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:141460200-141464000	Weak transcription	HSMMtube	muscle
32	chr3:141460200-141466000	Weak transcription	Ovary	ovary
33	chr3:141460200-141466400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:141460200-141468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:141460200-141468200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:141460200-141469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:141460400-141462000	Weak transcription	Brain Anterior Caudate	brain
38	chr3:141460400-141462200	Active TSS	GM12878-XiMat	blood
39	chr3:141460400-141463000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:141460400-141463000	Weak transcription	Adipose Nuclei	Adipose
41	chr3:141460400-141463200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:141460400-141463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:141460400-141463200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:141460400-141463400	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:141460400-141463400	Weak transcription	Left Ventricle	heart
46	chr3:141460400-141463400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:141460400-141463400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:141460400-141463600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:141460400-141463800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:141460400-141464000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links