Variant report

Variant	rs10411480
Chromosome Location	chr19:39324154-39324155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39320432-39324423	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
2	chr19:38805271..38808237-chr19:39322535..39325453,2	K562	blood:
3	chr19:39305126..39308258-chr19:39321941..39324366,4	K562	blood:
4	chr19:39138022..39142840-chr19:39322070..39325450,5	MCF-7	breast:
5	chr19:39224613..39228237-chr19:39319464..39324480,6	MCF-7	breast:
6	chr19:39323028..39324723-chr20:53082309..53085056,2	MCF-7	breast:

No data

Variant related genes	Relation type
ECH1	TF binding region
ENSG00000167645	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10403012	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10411844	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10425464	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426289	0.81[ASN][1000 genomes]
rs1078734	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11668179	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671711	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12974488	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12977821	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075587	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2075588	0.84[AMR][1000 genomes]
rs2116852	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278010	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35829996	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4328569	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802928	0.81[EUR][1000 genomes]
rs7248208	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110679	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs862454	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs862457	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862458	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862460	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862461	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs862462	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs862463	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9419	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10411480	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39322400-39331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39322600-39325400	Weak transcription	Esophagus	oesophagus
3	chr19:39322600-39325600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:39322600-39326200	Weak transcription	Gastric	stomach
5	chr19:39322600-39326400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:39322600-39326600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:39322600-39327400	Weak transcription	Small Intestine	intestine
8	chr19:39322800-39326200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:39322800-39326400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:39323000-39325400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:39323000-39325400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:39323000-39325400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:39323000-39326000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:39323000-39326000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:39323000-39326000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:39323000-39326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:39323000-39326000	Enhancers	Placenta	Placenta
18	chr19:39323000-39326200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39323000-39326200	Weak transcription	Fetal Brain Male	brain
20	chr19:39323000-39326200	Weak transcription	Ovary	ovary
21	chr19:39323000-39327200	Weak transcription	Brain Angular Gyrus	brain
22	chr19:39323000-39334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:39323200-39324200	Enhancers	A549	lung
24	chr19:39323200-39324600	Weak transcription	Fetal Brain Female	brain
25	chr19:39323200-39325200	Weak transcription	Primary T cells from cord blood	blood
26	chr19:39323200-39325400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:39323200-39325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:39323200-39325400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:39323200-39325400	Weak transcription	Fetal Thymus	thymus
30	chr19:39323200-39325400	Weak transcription	Thymus	Thymus
31	chr19:39323200-39325600	Weak transcription	Osteobl	bone
32	chr19:39323200-39326000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:39323200-39326000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:39323200-39326000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:39323200-39326000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:39323200-39326000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:39323200-39326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:39323200-39326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:39323200-39326000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:39323200-39326000	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:39323200-39326000	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:39323200-39326000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:39323200-39326000	Weak transcription	HSMM	muscle
44	chr19:39323200-39326000	Weak transcription	NH-A	brain
45	chr19:39323200-39326200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:39323200-39326200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr19:39323200-39326200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:39323200-39326200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr19:39323200-39326200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:39323200-39326200	Weak transcription	Brain Germinal Matrix	brain

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