Variant report

Variant	rs55912217
Chromosome Location	chr3:194789663-194789664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194789447..194796347-chr3:194796697..194800807,6	K562	blood:
2	chr3:194784787..194787485-chr3:194789648..194792559,2	K562	blood:
3	chr3:194787100..194789938-chr3:194793885..194796418,2	K562	blood:
4	chr3:194624572..194626596-chr3:194788748..194791365,2	K562	blood:
5	chr3:194405223..194406837-chr3:194788272..194790538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185112	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1389726	0.84[ASN][1000 genomes]
rs3796159	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781130	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55889329	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55958301	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56180618	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56324901	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56334245	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56343680	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57087537	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58473654	0.96[ASN][1000 genomes]
rs61376994	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6437453	0.98[ASN][1000 genomes]
rs6437454	0.98[ASN][1000 genomes]
rs66488008	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66707405	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67300447	0.88[ASN][1000 genomes]
rs6780281	0.88[ASN][1000 genomes]
rs6780283	0.88[ASN][1000 genomes]
rs6787005	0.99[ASN][1000 genomes]
rs6787114	0.99[ASN][1000 genomes]
rs6794037	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794986	0.91[ASN][1000 genomes]
rs6797948	0.91[ASN][1000 genomes]
rs6801456	0.99[ASN][1000 genomes]
rs6806857	0.98[ASN][1000 genomes]
rs9861985	0.84[ASN][1000 genomes]
rs9883940	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv1847174	chr3:194763601-194792415	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1848714	chr3:194785443-194792415	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194779000-194808000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:194780200-194800000	Weak transcription	Right Atrium	heart
3	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
4	chr3:194782000-194790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:194783400-194789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:194783600-194801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:194784000-194797800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:194784200-194790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:194784200-194797400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:194785200-194789800	Weak transcription	Aorta	Aorta
11	chr3:194785200-194796600	Weak transcription	NHLF	lung
12	chr3:194785400-194790200	Weak transcription	Esophagus	oesophagus
13	chr3:194785400-194793400	Weak transcription	Left Ventricle	heart
14	chr3:194785400-194799200	Weak transcription	Pancreas	Pancrea
15	chr3:194785600-194790000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:194785600-194791000	Weak transcription	Small Intestine	intestine
17	chr3:194785600-194792400	Weak transcription	Right Ventricle	heart
18	chr3:194785600-194801400	Weak transcription	Fetal Lung	lung
19	chr3:194785600-194801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:194785600-194802000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:194786000-194790600	Weak transcription	Stomach Mucosa	stomach
22	chr3:194786000-194791000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:194786000-194791000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:194786000-194796600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:194786000-194800400	Weak transcription	GM12878-XiMat	blood
26	chr3:194786800-194790600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:194786800-194791000	Weak transcription	Osteobl	bone
28	chr3:194787000-194789800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:194787200-194789800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:194787200-194800000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:194787400-194789800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:194787400-194790000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:194787400-194791000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:194787400-194791600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:194787400-194793800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:194787400-194795200	Strong transcription	Fetal Stomach	stomach
37	chr3:194787600-194789800	Weak transcription	Brain Germinal Matrix	brain
38	chr3:194787600-194790600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:194787600-194792600	Weak transcription	Brain Angular Gyrus	brain
40	chr3:194787600-194801000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:194787800-194790600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:194787800-194790600	Weak transcription	Fetal Intestine Large	intestine
43	chr3:194787800-194792200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:194787800-194794000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:194788000-194790600	Strong transcription	Fetal Thymus	thymus
46	chr3:194788000-194791000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:194788200-194790600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:194788200-194790600	Strong transcription	Fetal Intestine Small	intestine
49	chr3:194788200-194790800	Strong transcription	Gastric	stomach
50	chr3:194788200-194791600	Weak transcription	Brain Substantia Nigra	brain

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