Variant report

Variant	rs11119344
Chromosome Location	chr1:209943489-209943490
allele	A/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	chr1:209941568-209945214	GM18951	blood:	n/a	n/a
2	CTCF	chr1:209943418-209943577	K562	blood:	n/a	n/a
3	MAX	chr1:209941095-209944027	NB4	blood:	n/a	chr1:209943038-209943048 chr1:209943557-209943567
4	POLR2A	chr1:209941537-209945106	GM12892	blood:	n/a	n/a
5	CHD1	chr1:209941419-209943686	GM12878	blood:	n/a	n/a
6	EP300	chr1:209942216-209943822	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
8	RCOR1	chr1:209941534-209943537	GM12878	blood:	n/a	n/a
9	MTA3	chr1:209942612-209943814	GM12878	blood:	n/a	n/a
10	TCF12	chr1:209942145-209943901	SK-N-SH	brain:	n/a	chr1:209943560-209943570
11	POLR2A	chr1:209941560-209945629	GM12878	blood:	n/a	n/a
12	EP300	chr1:209942161-209943660	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr1:209943440-209943590	GM06990	blood:	n/a	n/a
14	MEF2A	chr1:209942334-209943787	SK-N-SH	brain:	n/a	chr1:209942839-209942854 chr1:209942838-209942859 chr1:209942840-209942854
15	EP300	chr1:209942218-209943867	SK-N-SH	brain:	n/a	n/a
16	MAZ	chr1:209941196-209943615	GM12878	blood:	n/a	chr1:209943038-209943048 chr1:209943557-209943567
17	CTCF	chr1:209943440-209943590	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr1:209943440-209943590	AoAF	blood vessel:	n/a	n/a
19	TEAD4	chr1:209943236-209943687	K562	blood:	n/a	n/a
20	NFATC1	chr1:209942405-209943549	GM12878	blood:	n/a	n/a
21	PML	chr1:209941415-209943747	GM12878	blood:	n/a	chr1:209941743-209941751
22	BCLAF1	chr1:209942673-209943490	GM12878	blood:	n/a	chr1:209942978-209942987 chr1:209943261-209943270
23	CTCF	chr1:209943394-209943733	GM12878	blood:	n/a	n/a
24	RUNX3	chr1:209943331-209943780	GM12878	blood:	n/a	n/a
25	MTA3	chr1:209941494-209944028	GM12878	blood:	n/a	n/a
26	CTCF	chr1:209943440-209943590	HPAF	blood vessel:	n/a	n/a
27	POLR2A	chr1:209941574-209945063	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:209941567-209945023	GM18526	blood:	n/a	n/a
29	FOSL2	chr1:209942420-209943674	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
31	CTCF	chr1:209943400-209943550	HPAF	blood vessel:	n/a	n/a
32	CTCF	chr1:209943460-209943610	HVMF	connective:	n/a	n/a
33	ZNF143	chr1:209942620-209943568	GM12878	blood:	n/a	chr1:209942983-209943001
34	POLR2A	chr1:209942381-209945631	GM12892	blood:	n/a	n/a
35	GATA3	chr1:209942300-209943875	SK-N-SH	brain:	n/a	chr1:209942977-209942987
36	NFIC	chr1:209942017-209943748	SK-N-SH	brain:	n/a	n/a
37	FOXM1	chr1:209942437-209943725	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr1:209942340-209943766	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:209941597-209945746	GM19099	blood:	n/a	n/a
41	POLR2A	chr1:209941520-209945190	GM15510	blood:	n/a	n/a
42	GATA2	chr1:209942702-209943664	HUVEC	blood vessel:	n/a	chr1:209942977-209942987
43	POLR2A	chr1:209942360-209945616	GM12892	blood:	n/a	n/a
44	CTCF	chr1:209943480-209943630	HBMEC	blood vessel:	n/a	n/a
45	JUND	chr1:209942338-209943763	SK-N-SH	brain:	n/a	n/a
46	TEAD4	chr1:209942321-209943779	SK-N-SH	brain:	n/a	n/a
47	ZEB1	chr1:209943163-209945525	GM12878	blood:	n/a	n/a
48	CTCF	chr1:209943420-209943570	HA-sp	spinal cord:	n/a	n/a
49	POLR2A	chr1:209942521-209944174	GM12878	blood:	n/a	n/a
50	CHD2	chr1:209941614-209943541	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209931478..209933302-chr1:209941660..209944063,2	K562	blood:
2	chr1:209943015..209945017-chr1:209946674..209949825,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-4	chr1:209943366-209944059	NONHSAT009235

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11582607	0.84[CEU][hapmap]
rs17389541	0.84[CEU][hapmap]
rs2013196	0.84[CEU][hapmap]
rs6660087	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6699507	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3429215	chr1:209942329-209947327	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3449118	chr1:209942529-209946727	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3393757	chr1:209943129-209946427	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	esv3375148	chr1:209943179-209945677	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11119344	IRF6	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209931000-209943600	Weak transcription	Gastric	stomach
2	chr1:209940600-209943600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:209940600-209944200	Flanking Active TSS	Dnd41	blood
4	chr1:209940800-209943800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:209940800-209943800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:209940800-209944000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:209940800-209944000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:209940800-209944000	Enhancers	HMEC	breast
9	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
10	chr1:209941000-209944000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:209941000-209945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:209941400-209943600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:209941400-209943800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:209941400-209943800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:209941400-209943800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:209941400-209944200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr1:209941400-209944400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:209941400-209945000	Flanking Active TSS	GM12878-XiMat	blood
19	chr1:209941600-209943600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:209941600-209943600	Active TSS	Thymus	Thymus
21	chr1:209941600-209943800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:209941600-209943800	Enhancers	Brain Hippocampus Middle	brain
23	chr1:209941600-209943800	Enhancers	Fetal Muscle Leg	muscle
24	chr1:209941600-209944000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:209941600-209944200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:209941600-209944400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:209941600-209944400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr1:209941800-209943600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:209941800-209943600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr1:209941800-209943600	Enhancers	Fetal Lung	lung
31	chr1:209941800-209943800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:209941800-209943800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:209941800-209944000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr1:209941800-209944600	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr1:209941800-209944800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:209941800-209945000	Enhancers	Left Ventricle	heart
37	chr1:209942000-209943800	Enhancers	Pancreas	Pancrea
38	chr1:209942000-209943800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:209942000-209944000	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:209942000-209944000	Enhancers	HUVEC	blood vessel
41	chr1:209942000-209944200	Enhancers	NHLF	lung
42	chr1:209942000-209944800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:209942000-209944800	Enhancers	Brain Substantia Nigra	brain
44	chr1:209942000-209945400	Enhancers	Placenta	Placenta
45	chr1:209942200-209943600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:209942200-209943800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:209942200-209943800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:209942200-209943800	Enhancers	Spleen	Spleen
49	chr1:209942400-209943600	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:209942400-209943800	Active TSS	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links