Variant report

Variant	rs71354996
Chromosome Location	chr19:38809359-38809360
allele	A/C
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	JUND	chr19:38809301-38809379	K562	blood:	n/a	n/a
2	POLR2A	chr19:38809269-38809480	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38808796..38810665-chr19:38878393..38880605,3	MCF-7	breast:
2	chr19:38805479..38807784-chr19:38808635..38810282,2	K562	blood:
3	chr19:38806332..38809400-chr19:38825014..38828541,5	K562	blood:
4	chr19:38746183..38748575-chr19:38806704..38809483,2	K562	blood:
5	chr19:38753833..38757251-chr19:38808796..38812283,9	MCF-7	breast:
6	chr19:38745470..38748025-chr19:38806544..38809528,4	K562	blood:

No data

Variant related genes	Relation type
KCNK6	TF binding region
YIF1B	TF binding region
ENSG00000167642	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167641	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11878707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12460599	0.82[AFR][1000 genomes]
rs34614180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35077481	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35323359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35710536	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3859550	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7253827	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38806400-38810200	Enhancers	Fetal Heart	heart
2	chr19:38807000-38809800	Weak transcription	Gastric	stomach
3	chr19:38807000-38809800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:38807000-38810000	Weak transcription	HSMMtube	muscle
5	chr19:38807200-38809400	Weak transcription	Left Ventricle	heart
6	chr19:38807200-38809400	Weak transcription	NHLF	lung
7	chr19:38807200-38809600	Weak transcription	Pancreas	Pancrea
8	chr19:38807200-38809800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:38807200-38809800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:38807200-38809800	Weak transcription	Aorta	Aorta
11	chr19:38807200-38809800	Weak transcription	Small Intestine	intestine
12	chr19:38807200-38809800	Enhancers	HUVEC	blood vessel
13	chr19:38807200-38809800	Weak transcription	Osteobl	bone
14	chr19:38807200-38810000	Weak transcription	Ovary	ovary
15	chr19:38807400-38809600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr19:38807400-38809800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:38807400-38809800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:38807400-38809800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:38807400-38809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:38807400-38809800	Weak transcription	Brain Angular Gyrus	brain
21	chr19:38807400-38809800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:38807400-38809800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:38807600-38810000	Weak transcription	Brain Substantia Nigra	brain
24	chr19:38807800-38809400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:38807800-38809600	Weak transcription	Brain Anterior Caudate	brain
26	chr19:38807800-38809600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:38808000-38809400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:38808000-38809400	Weak transcription	Esophagus	oesophagus
29	chr19:38808000-38809400	Weak transcription	Stomach Mucosa	stomach
30	chr19:38808000-38809600	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:38808000-38809800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:38808000-38809800	Weak transcription	Lung	lung
33	chr19:38808000-38810000	Weak transcription	Psoas Muscle	Psoas
34	chr19:38808000-38810200	Enhancers	Primary hematopoietic stem cells	blood
35	chr19:38808200-38809400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:38808200-38809400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:38808200-38809400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:38808200-38809600	Weak transcription	Colonic Mucosa	Colon
39	chr19:38808200-38809800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr19:38808200-38809800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr19:38808200-38809800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr19:38808200-38810000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr19:38808200-38810000	Enhancers	Primary B cells from peripheral blood	blood
44	chr19:38808200-38810000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr19:38808200-38810000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr19:38808200-38810000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:38808200-38810000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:38808400-38809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:38808400-38809600	Weak transcription	Primary T cells from cord blood	blood
50	chr19:38808400-38809800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links