Variant report

Variant	rs12461700
Chromosome Location	chr19:38829013-38829014
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
2	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
3	chr19:38753791..38756428-chr19:38824915..38829046,7	MCF-7	breast:
4	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
5	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
6	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
7	chr19:38826489..38830578-chr19:38835148..38838719,4	K562	blood:
8	chr19:38825745..38829204-chr19:38906597..38909224,3	K562	blood:
9	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
10	chr19:38827274..38829284-chr19:38833779..38835815,2	MCF-7	breast:
11	chr19:38826766..38829028-chr19:38851929..38854753,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179168	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1060455	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11083453	0.83[AMR][1000 genomes]
rs12460181	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460264	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12460599	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12461248	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462230	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12463175	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2072350	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2074979	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2074980	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286547	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286550	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286551	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2302226	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34614180	0.84[AFR][1000 genomes]
rs35323359	0.84[AFR][1000 genomes]
rs35848839	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745955	0.93[ASN][1000 genomes]
rs3745956	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3745960	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3745961	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3745962	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60577771	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60759642	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60915799	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61379500	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38827800-38829600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:38828000-38830600	Enhancers	Placenta	Placenta
3	chr19:38828000-38833400	Weak transcription	Aorta	Aorta
4	chr19:38828000-38834600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:38828000-38838400	Weak transcription	HSMMtube	muscle
6	chr19:38828200-38829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:38828200-38829200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:38828200-38829200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:38828200-38829200	Weak transcription	Fetal Brain Female	brain
10	chr19:38828200-38829400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38828200-38829400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:38828200-38829400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:38828200-38829400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr19:38828200-38829400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr19:38828200-38829400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:38828200-38829400	Enhancers	Pancreas	Pancrea
17	chr19:38828200-38829600	Weak transcription	Fetal Intestine Large	intestine
18	chr19:38828200-38829600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:38828200-38829600	Weak transcription	NHEK	skin
20	chr19:38828200-38831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:38828200-38831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:38828200-38831800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr19:38828200-38833200	Weak transcription	Lung	lung
24	chr19:38828200-38833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:38828200-38833400	Weak transcription	Spleen	Spleen
26	chr19:38828200-38833800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:38828200-38834000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:38828200-38834000	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:38828200-38834600	Weak transcription	Gastric	stomach
30	chr19:38828200-38834800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:38828200-38836400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:38828200-38836600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38828200-38836800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:38828200-38837000	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:38828200-38837400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:38828200-38838000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr19:38828200-38838200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr19:38828200-38838400	Weak transcription	Colonic Mucosa	Colon
39	chr19:38828200-38838400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:38828200-38839000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:38828200-38840400	Weak transcription	Left Ventricle	heart
42	chr19:38828200-38841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:38828200-38842000	Weak transcription	Brain Angular Gyrus	brain
44	chr19:38828200-38842600	Weak transcription	Esophagus	oesophagus
45	chr19:38828200-38844800	Weak transcription	Brain Substantia Nigra	brain
46	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
47	chr19:38828400-38829200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:38828400-38829200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:38828400-38829200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:38828400-38829200	Weak transcription	Fetal Intestine Small	intestine

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