Variant report

Variant	rs1334926
Chromosome Location	chr6:119400716-119400717
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	NFIC	chr6:119400347-119400871	SK-N-SH	brain:	n/a	chr6:119400602-119400618
2	NFIC	chr6:119400292-119400935	ECC-1	luminal epithelium:	n/a	chr6:119400602-119400618 chr6:119400867-119400895
3	NFIC	chr6:119399912-119401209	ECC-1	luminal epithelium:	n/a	chr6:119400602-119400618 chr6:119400867-119400895
4	NFIC	chr6:119399962-119400979	SK-N-SH	brain:	n/a	chr6:119400602-119400618 chr6:119400867-119400895
5	MYC	chr6:119399683-119401040	K562	blood:	n/a	chr6:119400367-119400377
6	FOS	chr6:119400537-119400730	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr6:119399758-119400785	K562	blood:	n/a	chr6:119400367-119400377
8	ZNF263	chr6:119397251-119400847	HEK293-T-REx	kidney:	n/a	chr6:119399834-119399843
9	FOS	chr6:119400449-119400773	MCF10A-Er-Src	breast:	n/a	chr6:119400746-119400753 chr6:119400744-119400753
10	MYC	chr6:119400562-119400735	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119253238..119258280-chr6:119398045..119402661,8	K562	blood:
2	chr6:119398174..119401168-chr6:119668507..119671059,2	K562	blood:
3	chr6:119255727..119258203-chr6:119400226..119402388,2	K562	blood:
4	chr6:119213805..119216904-chr6:119398441..119401842,5	K562	blood:
5	chr6:119340150..119341982-chr6:119399183..119401577,2	K562	blood:

Variant related genes	Relation type
FAM184A	TF binding region
ENSG00000111885	Chromatin interaction
ENSG00000111875	Chromatin interaction
ENSG00000253194	Chromatin interaction
ENSG00000111879	Chromatin interaction
ENSG00000111877	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10080387	0.90[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10081010	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1334925	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1413908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1591367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2146762	0.90[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs2209039	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4579389	0.84[EUR][1000 genomes]
rs62421122	0.84[EUR][1000 genomes]
rs62421156	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1334926	TSPYL1	cis	parietal	SCAN
rs1334926	MAN1A1	cis	lymphoblastoid	seeQTL
rs1334926	C6orf204	cis	cerebellum	SCAN
rs1334926	MCM9	cis	cerebellum	SCAN
rs1334926	FAM184A	cis	parietal	SCAN
rs1334926	MCM9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119397400-119400800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:119398000-119400800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:119398000-119401000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:119398200-119400800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:119398200-119400800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:119398400-119400800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:119398400-119401000	Active TSS	Ovary	ovary
8	chr6:119398400-119401200	Active TSS	Stomach Smooth Muscle	stomach
9	chr6:119398600-119401000	Active TSS	Right Atrium	heart
10	chr6:119398800-119400800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:119398800-119400800	Active TSS	Fetal Kidney	kidney
12	chr6:119398800-119401000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:119399000-119400800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr6:119399000-119400800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr6:119399000-119400800	Active TSS	Brain Anterior Caudate	brain
16	chr6:119399000-119400800	Bivalent/Poised TSS	A549	lung
17	chr6:119399000-119400800	Bivalent/Poised TSS	HSMMtube	muscle
18	chr6:119399200-119400800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:119399200-119400800	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr6:119399200-119400800	Active TSS	Brain Substantia Nigra	brain
21	chr6:119399400-119400800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:119399400-119400800	Active TSS	Fetal Intestine Large	intestine
23	chr6:119399400-119400800	Active TSS	Fetal Muscle Trunk	muscle
24	chr6:119399400-119400800	Active TSS	Fetal Muscle Leg	muscle
25	chr6:119399400-119400800	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr6:119399400-119400800	Active TSS	Psoas Muscle	Psoas
27	chr6:119399400-119401000	Active TSS	Aorta	Aorta
28	chr6:119399400-119401000	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr6:119399400-119401000	Active TSS	NHDF-Ad	bronchial
30	chr6:119399600-119400800	Active TSS	Right Ventricle	heart
31	chr6:119399600-119400800	Active TSS	NHLF	lung
32	chr6:119399800-119400800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:119399800-119400800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:119399800-119400800	Active TSS	Colonic Mucosa	Colon
35	chr6:119400000-119400800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:119400000-119400800	Flanking Active TSS	NH-A	brain
37	chr6:119400200-119400800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
38	chr6:119400200-119400800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
39	chr6:119400200-119400800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
40	chr6:119400200-119400800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
41	chr6:119400200-119400800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr6:119400200-119400800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:119400200-119400800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:119400200-119400800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr6:119400200-119400800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr6:119400200-119400800	Flanking Active TSS	HUVEC	blood vessel
47	chr6:119400200-119401000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:119400200-119401000	Flanking Bivalent TSS/Enh	HepG2	liver
49	chr6:119400200-119401000	Flanking Active TSS	NHEK	skin
50	chr6:119400200-119401200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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