Variant report

Variant	rs6549183
Chromosome Location	chr3:69140343-69140344
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69135075..69137300-chr3:69139396..69142710,3	MCF-7	breast:
2	chr3:69133113..69136938-chr3:69139161..69143786,5	K562	blood:
3	chr3:69139238..69140744-chr3:69142912..69145095,2	MCF-7	breast:
4	chr3:69138840..69141310-chr3:69150694..69152337,2	MCF-7	breast:
5	chr3:69127883..69130240-chr3:69139451..69142442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12054081	0.90[ASN][1000 genomes]
rs17005397	0.83[EUR][1000 genomes]
rs17005400	0.83[EUR][1000 genomes]
rs4615083	0.83[EUR][1000 genomes]
rs4855355	0.83[EUR][1000 genomes]
rs5017791	0.83[EUR][1000 genomes]
rs5017792	0.83[EUR][1000 genomes]
rs55978846	0.83[EUR][1000 genomes]
rs58798960	0.83[EUR][1000 genomes]
rs60204248	0.83[EUR][1000 genomes]
rs61207882	0.83[EUR][1000 genomes]
rs72924865	0.90[ASN][1000 genomes]
rs72924866	0.90[ASN][1000 genomes]
rs72924867	0.90[ASN][1000 genomes]
rs72924873	0.90[ASN][1000 genomes]
rs72924874	0.90[ASN][1000 genomes]
rs72924875	0.90[ASN][1000 genomes]
rs72924876	0.90[ASN][1000 genomes]
rs72924880	0.90[ASN][1000 genomes]
rs7621852	0.90[ASN][1000 genomes]
rs937863	0.83[EUR][1000 genomes]
rs9825485	0.83[EUR][1000 genomes]
rs9843043	0.83[EUR][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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69135200-69155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:69135600-69140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:69135800-69140800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:69135800-69141200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:69135800-69141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:69135800-69141200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:69135800-69141200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:69135800-69141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:69135800-69155800	Weak transcription	Fetal Kidney	kidney
10	chr3:69136000-69142400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:69136000-69143800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:69136200-69141400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:69136400-69140400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:69136400-69140800	Weak transcription	Fetal Brain Female	brain
15	chr3:69136400-69141000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:69136600-69147000	Enhancers	Colon Smooth Muscle	Colon
17	chr3:69136800-69143200	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:69136800-69156400	Weak transcription	Fetal Brain Male	brain
19	chr3:69137200-69143000	Enhancers	Placenta	Placenta
20	chr3:69137200-69145200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:69137400-69141000	Genic enhancers	Fetal Thymus	thymus
22	chr3:69137600-69141600	Enhancers	HMEC	breast
23	chr3:69137600-69145200	Genic enhancers	HSMM	muscle
24	chr3:69137800-69140600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:69137800-69140800	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr3:69137800-69140800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
27	chr3:69137800-69143200	Enhancers	Brain Angular Gyrus	brain
28	chr3:69138000-69140400	Genic enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:69138000-69140400	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr3:69138000-69140600	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:69138000-69140800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:69138000-69140800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:69138000-69141200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:69138000-69141400	Weak transcription	Brain Germinal Matrix	brain
35	chr3:69138000-69141400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:69138000-69141400	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:69138200-69140800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:69138200-69140800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:69138200-69140800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:69138200-69141200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:69138200-69143200	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:69138200-69143200	Weak transcription	Ovary	ovary
43	chr3:69138400-69141200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:69138600-69145600	Enhancers	Stomach Mucosa	stomach
45	chr3:69139000-69140800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr3:69139200-69140600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:69139200-69140600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:69139200-69140600	Enhancers	Brain Anterior Caudate	brain
49	chr3:69139200-69140600	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:69139200-69140600	Genic enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links