Variant report

Variant	rs236349
Chromosome Location	chr6:36820565-36820566
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:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36818424..36822217-chr6:36952499..36954853,3	K562	blood:
2	chr6:36815130..36818530-chr6:36818954..36823604,5	K562	blood:
3	chr6:36818402..36820845-chr6:36839633..36841729,2	K562	blood:
4	chr6:36819964..36824038-chr6:36826260..36830015,5	MCF-7	breast:
5	chr6:36819191..36821393-chr6:36826640..36829329,2	MCF-7	breast:
6	chr6:36811312..36813099-chr6:36818892..36821190,2	MCF-7	breast:
7	chr6:36820493..36822217-chr6:36952499..36954085,2	K562	blood:
8	chr6:36819209..36822564-chr6:36824095..36826600,3	K562	blood:
9	chr6:36733851..36734590-chr6:36820298..36821123,2	K562	blood:
10	chr6:36742135..36744958-chr6:36819478..36821110,2	K562	blood:
11	chr6:36818579..36822639-chr6:36835896..36837920,3	K562	blood:
12	chr6:36818002..36820596-chr6:36841531..36843370,2	K562	blood:
13	chr6:36816699..36818320-chr6:36819945..36822001,2	MCF-7	breast:
14	chr6:36818907..36820999-chr6:36822300..36824076,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPIL1-1	chr6:36819837-36822439	NONHSAT112236

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000137168	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2116447	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2293393	0.84[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap]
rs2303993	0.87[ASN][1000 genomes]
rs236352	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236385	0.84[JPT][hapmap]
rs236386	0.84[JPT][hapmap]
rs3756905	0.87[ASN][1000 genomes]
rs3778016	0.87[ASN][1000 genomes]
rs3778017	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3846871	0.89[ASN][1000 genomes]
rs449840	0.82[ASN][1000 genomes]
rs4594944	0.88[TSI][hapmap]
rs460539	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4714018	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs58214515	0.86[ASN][1000 genomes]
rs62406643	0.86[ASN][1000 genomes]
rs6909988	0.87[ASN][1000 genomes]
rs6910832	0.81[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6914008	0.87[ASN][1000 genomes]
rs6934844	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9366920	0.85[ASN][1000 genomes]
rs9368966	0.89[ASN][1000 genomes]
rs9380616	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9380618	0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9470426	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs236349	GLP1R	cis	parietal	SCAN
rs236349	LRFN2	cis	cerebellum	SCAN
rs236349	PPIL1	Cis_1M	lymphoblastoid	RTeQTL
rs236349	PPIL1	cis	Stomach	GTEx
rs236349	PNPLA1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
3	chr6:36813200-36821200	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:36813200-36823200	Weak transcription	Brain Substantia Nigra	brain
5	chr6:36816600-36823000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:36816800-36821800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:36817000-36821400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:36817000-36823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:36817000-36826200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
11	chr6:36817200-36820600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:36817200-36821200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:36817200-36823200	Weak transcription	Gastric	stomach
14	chr6:36817200-36823200	Weak transcription	Pancreas	Pancrea
15	chr6:36817200-36823600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:36817200-36830200	Weak transcription	Fetal Lung	lung
17	chr6:36817200-36833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
19	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
20	chr6:36817400-36820800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:36817400-36821400	Enhancers	Fetal Heart	heart
22	chr6:36817600-36821000	Weak transcription	Fetal Intestine Large	intestine
23	chr6:36817600-36821200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:36817600-36822400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:36818000-36821400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:36818000-36821400	Enhancers	Left Ventricle	heart
27	chr6:36818000-36822800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:36818000-36824800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:36818200-36822200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:36818400-36821000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:36818400-36821600	Enhancers	Colon Smooth Muscle	Colon
32	chr6:36818400-36821800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:36818600-36821600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:36818600-36822200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:36818800-36820800	Enhancers	NHLF	lung
36	chr6:36818800-36821400	Enhancers	HSMM	muscle
37	chr6:36818800-36821800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:36818800-36821800	Enhancers	Osteobl	bone
39	chr6:36818800-36822400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:36819000-36820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:36819000-36820600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:36819000-36820600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:36819000-36820800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:36819000-36822000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr6:36819000-36823000	Weak transcription	Lung	lung
46	chr6:36819000-36830000	Weak transcription	Fetal Kidney	kidney
47	chr6:36819000-36840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:36819200-36820600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:36819200-36820600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:36819200-36821200	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links