Variant report

Variant	rs627346
Chromosome Location	chr18:29656956-29656957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:29656613-29656978	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29654269..29657288-chr18:29670351..29673351,3	K562	blood:
2	chr18:29656745..29659248-chr18:29670363..29672023,2	K562	blood:

Variant related genes	Relation type
ENSG00000214917	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs4799325	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4799628	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs61392417	0.83[EUR][1000 genomes]
rs889888	0.81[EUR][1000 genomes]
rs9955978	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs9962565	0.83[EUR][1000 genomes]
rs9967524	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061305	chr18:29609935-29664528	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1064505	chr18:29637586-29659148	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv909520	chr18:29645496-29666127	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv909521	chr18:29645496-29671510	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv978625	chr18:29654097-29659754	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs627346	RNF138	cis	Esophagus Mucosa	GTEx
rs627346	RNF138	cis	multi-tissue	Pritchard
rs627346	RNF138	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29602600-29664200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr18:29626000-29657200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr18:29630000-29664400	Weak transcription	Fetal Muscle Leg	muscle
4	chr18:29630400-29664400	Weak transcription	Left Ventricle	heart
5	chr18:29630800-29658600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr18:29631400-29671400	Weak transcription	Hela-S3	cervix
7	chr18:29640400-29664400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr18:29640400-29664600	Weak transcription	Thymus	Thymus
9	chr18:29640600-29664600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr18:29642600-29664600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:29644000-29664200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:29647000-29660200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr18:29647000-29660400	Weak transcription	Fetal Thymus	thymus
14	chr18:29647000-29664400	Weak transcription	Liver	Liver
15	chr18:29648400-29664200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr18:29648400-29664400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr18:29648600-29664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr18:29648800-29658200	Weak transcription	Fetal Intestine Large	intestine
19	chr18:29649000-29664200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr18:29650000-29663000	Weak transcription	Adipose Nuclei	Adipose
21	chr18:29652200-29660400	Weak transcription	Fetal Intestine Small	intestine
22	chr18:29652800-29663600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr18:29654200-29664200	Weak transcription	Primary B cells from cord blood	blood
24	chr18:29654400-29660400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr18:29654400-29660400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr18:29654400-29661000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr18:29654400-29663600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr18:29654400-29664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr18:29654400-29664400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr18:29654600-29662800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr18:29654600-29663800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr18:29654600-29663800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr18:29654600-29664400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr18:29655200-29663000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:29655400-29664200	Weak transcription	Primary T cells from cord blood	blood
36	chr18:29655800-29663600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:29656000-29671400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:29656200-29664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr18:29656400-29663200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr18:29656800-29664000	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links