Variant report

Variant	rs6914008
Chromosome Location	chr6:36853037-36853038
allele	A/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	CTCF	chr6:36852920-36853070	GM12866	blood:	n/a	n/a
2	EP300	chr6:36853032-36854336	K562	blood:	n/a	n/a
3	CBX3	chr6:36852892-36854233	K562	blood:	n/a	n/a
4	HCFC1	chr6:36852922-36854602	Hela-S3	cervix:	n/a	n/a
5	SMC3	chr6:36852755-36854422	SK-N-SH	brain:	n/a	chr6:36853553-36853567
6	MTA3	chr6:36852854-36854232	GM12878	blood:	n/a	n/a
7	PML	chr6:36852953-36854190	GM12878	blood:	n/a	n/a
8	CTCF	chr6:36852989-36854168	SK-N-SH	brain:	n/a	chr6:36853552-36853568
9	CTCF	chr6:36853004-36853957	HCT-116	colon:	n/a	chr6:36853552-36853568
10	CTCF	chr6:36853020-36853170	HMF	breast:	n/a	n/a
11	POLR2A	chr6:36852951-36853160	HepG2	liver:	n/a	n/a
12	NR2F2	chr6:36852975-36854922	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36841771..36843991-chr6:36852556..36855136,3	MCF-7	breast:
2	chr6:36852278..36855515-chr6:36952430..36957026,4	MCF-7	breast:
3	chr6:36803997..36809047-chr6:36852852..36856509,4	K562	blood:
4	chr6:36852138..36856054-chr6:36953606..36956862,5	K562	blood:
5	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:

Variant related genes	Relation type
C6orf89	TF binding region
ENSG00000137409	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1150784	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2116447	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293393	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303993	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236349	0.87[ASN][1000 genomes]
rs236352	0.96[ASN][1000 genomes]
rs3756905	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778016	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778017	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846871	0.95[ASN][1000 genomes]
rs449840	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4594944	0.82[ASN][1000 genomes]
rs4714018	0.95[ASN][1000 genomes]
rs58214515	0.96[ASN][1000 genomes]
rs62406643	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457963	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6909988	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910832	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6934844	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8472	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366920	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9368966	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380616	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9380618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380626	0.86[ASN][1000 genomes]
rs9462233	0.84[AFR][1000 genomes]
rs9470426	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	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
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6914008	PPIL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36850400-36853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:36852600-36853200	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:36852600-36853200	Enhancers	Primary T cells from cord blood	blood
4	chr6:36852600-36853200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:36852600-36853200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:36852600-36853200	Enhancers	Fetal Heart	heart
7	chr6:36852800-36853200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:36852800-36853200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:36852800-36853200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:36852800-36853200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:36853000-36853200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:36853000-36853200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:36853000-36853200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:36853000-36853200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:36853000-36853200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:36853000-36853200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:36853000-36853200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:36853000-36853200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:36853000-36853200	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:36853000-36853200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:36853000-36853200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:36853000-36853200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:36853000-36853200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:36853000-36853200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:36853000-36853200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:36853000-36853200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:36853000-36853200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:36853000-36853200	Enhancers	Adipose Nuclei	Adipose
29	chr6:36853000-36853200	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr6:36853000-36853200	Enhancers	Brain Substantia Nigra	brain
31	chr6:36853000-36853200	Enhancers	Duodenum Mucosa	Duodenum
32	chr6:36853000-36853200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:36853000-36853200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:36853000-36853200	Enhancers	Fetal Brain Male	brain
35	chr6:36853000-36853200	Enhancers	Fetal Intestine Large	intestine
36	chr6:36853000-36853200	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr6:36853000-36853200	Enhancers	Fetal Lung	lung
38	chr6:36853000-36853200	Enhancers	Fetal Muscle Leg	muscle
39	chr6:36853000-36853200	Enhancers	Placenta	Placenta
40	chr6:36853000-36853200	Enhancers	Fetal Stomach	stomach
41	chr6:36853000-36853200	Enhancers	Fetal Thymus	thymus
42	chr6:36853000-36853200	Enhancers	Left Ventricle	heart
43	chr6:36853000-36853200	Enhancers	Pancreas	Pancrea
44	chr6:36853000-36853200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:36853000-36853200	Enhancers	Right Ventricle	heart
46	chr6:36853000-36853200	Enhancers	Small Intestine	intestine
47	chr6:36853000-36853200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr6:36853000-36853200	Enhancers	HMEC	breast
49	chr6:36853000-36853200	Enhancers	NHEK	skin
50	chr6:36853000-36853200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links