Variant report

Variant	rs35969918
Chromosome Location	chr6:109763040-109763041
allele	C/G
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	chr6:109761401-109763076	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:109761435-109763358	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr6:109760621-109763112	SK-N-SH	brain:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
4	POLR2A	chr6:109761570-109763535	GM15510	blood:	n/a	n/a
5	MTA3	chr6:109762965-109763438	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:109762529-109763068	GM12892	blood:	n/a	n/a
7	MTA3	chr6:109761441-109764372	GM12878	blood:	n/a	n/a
8	MAX	chr6:109761267-109763135	HCT-116	colon:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
9	ZNF263	chr6:109761658-109764349	HEK293-T-REx	kidney:	n/a	chr6:109762432-109762441 chr6:109762690-109762699 chr6:109764290-109764299
10	POLR2A	chr6:109761840-109763069	GM12878	blood:	n/a	n/a
11	STAT5A	chr6:109761824-109763785	GM12878	blood:	n/a	chr6:109763295-109763307 chr6:109762900-109762908 chr6:109763111-109763123
12	PML	chr6:109761384-109764341	GM12878	blood:	n/a	chr6:109763129-109763137 chr6:109761642-109761650
13	POLR2A	chr6:109762774-109764553	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr6:109761754-109765661	GM12878	blood:	n/a	n/a
15	MAZ	chr6:109761290-109763147	IMR90	lung:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
16	POLR2A	chr6:109761298-109765076	H1-hESC	embryonic stem cell:	n/a	n/a
17	RUNX3	chr6:109761372-109763059	GM12878	blood:	n/a	chr6:109762385-109762400
18	POLR2A	chr6:109761500-109772072	GM12892	blood:	n/a	n/a
19	MAX	chr6:109761318-109763047	HepG2	liver:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
20	POLR2A	chr6:109762138-109763046	GM12892	blood:	n/a	n/a
21	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
23	POLR2A	chr6:109762084-109763100	GM12892	blood:	n/a	n/a
24	POLR2A	chr6:109761331-109763094	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr6:109761608-109765621	GM12878	blood:	n/a	n/a
26	RELA	chr6:109761777-109763130	GM19099	blood:	n/a	chr6:109762471-109762480 chr6:109762471-109762480

No.	Distal block	Cell Line	Cell type
1	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
2	chr6:109414651..109418067-chr6:109760738..109763991,4	MCF-7	breast:
3	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
4	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
5	chr6:109699708..109703613-chr6:109762807..109765058,4	K562	blood:
6	chr6:108880181..108882285-chr6:109761167..109763162,2	MCF-7	breast:
7	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
8	chr6:109760146..109763576-chr6:109804047..109805770,3	MCF-7	breast:
9	chr6:109752212..109757242-chr6:109759553..109764133,7	MCF-7	breast:

Variant related genes	Relation type
SMPD2	TF binding region
PPIL6	TF binding region
ENSG00000185250	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000239160	Chromatin interaction
ENSG00000118689	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11753645	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11757877	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12524502	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12528566	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528712	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13192476	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13195517	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199519	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13203252	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1322818	0.80[AMR][1000 genomes]
rs2275652	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34131679	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34292461	0.80[AMR][1000 genomes]
rs34320275	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34533653	0.80[AMR][1000 genomes]
rs35452836	0.81[EUR][1000 genomes]
rs3757238	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799835	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799840	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4428538	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61076041	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61233650	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61318425	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67857472	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6929208	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35969918	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs35969918	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs35969918	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs35969918	SMPD2	cis	Whole Blood	GTEx
rs35969918	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109760200-109763200	Active TSS	A549	lung
2	chr6:109760400-109763400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:109761200-109763200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:109761200-109763400	Active TSS	HSMMtube	muscle
5	chr6:109761400-109763400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:109762200-109763200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr6:109762200-109763200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:109762200-109763200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr6:109762200-109763200	Flanking Active TSS	Fetal Brain Female	brain
10	chr6:109762200-109763200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr6:109762200-109763400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr6:109762200-109763600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr6:109762400-109763200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:109762400-109763200	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr6:109762400-109763200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr6:109762400-109763200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr6:109762400-109763200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr6:109762400-109763200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:109762400-109763200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:109762400-109763200	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr6:109762400-109763200	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr6:109762400-109763200	Flanking Active TSS	Placenta	Placenta
23	chr6:109762400-109763200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:109762400-109763200	Flanking Active TSS	HSMM	muscle
25	chr6:109762400-109763200	Flanking Active TSS	NHEK	skin
26	chr6:109762400-109763200	Flanking Active TSS	Osteobl	bone
27	chr6:109762400-109763400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:109762400-109763400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:109762400-109763400	Flanking Active TSS	Colonic Mucosa	Colon
30	chr6:109762400-109763400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr6:109762400-109763400	Flanking Active TSS	Dnd41	blood
32	chr6:109762400-109763400	Flanking Active TSS	HMEC	breast
33	chr6:109762400-109763600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr6:109762400-109763600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr6:109762600-109763200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr6:109762600-109763200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:109762600-109763200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:109762600-109763200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:109762600-109763200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:109762600-109763200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:109762600-109763200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:109762600-109763200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:109762600-109763200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr6:109762600-109763200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:109762600-109763200	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr6:109762600-109763200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr6:109762600-109763200	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr6:109762600-109763200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr6:109762600-109763200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr6:109762600-109763200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links