Variant report

Variant	rs11119340
Chromosome Location	chr1:209940560-209940561
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	BATF	chr1:209940502-209940754	GM12878	blood:	n/a	chr1:209940708-209940717

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209940429..209942619-chr1:209957623..209959222,2	MCF-7	breast:

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1000283	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs1007693	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs10157973	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs10863786	0.84[CEU][hapmap]
rs11119327	0.81[CEU][hapmap]
rs11119328	0.87[MEX][hapmap]
rs11119336	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11119338	1.00[JPT][hapmap]
rs11119341	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807619	0.93[MEX][hapmap]
rs12034758	0.82[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12059226	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs12094117	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs12120361	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs12131636	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415542	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs17015169	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs17389184	0.81[CHD][hapmap];0.93[MEX][hapmap]
rs17389198	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2272867	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs28767240	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3753606	0.91[CEU][hapmap];0.82[MEX][hapmap]
rs3766619	0.81[CEU][hapmap]
rs4990735	0.88[EUR][1000 genomes]
rs611861	0.86[CEU][hapmap]
rs627670	0.85[CEU][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs6540549	0.81[CEU][hapmap]
rs6540550	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs6540553	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs6540554	0.81[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs654984	0.91[CEU][hapmap]
rs6665715	0.85[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs6672256	1.00[MEX][hapmap]
rs6679405	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs6685077	0.86[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs6702301	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs7539852	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs909710	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs932335	0.81[CEU][hapmap]
rs9430012	0.81[CEU][hapmap]
rs9430016	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs9430017	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11119340	IRF6	cis	cerebellum	SCAN
rs11119340	HSD11B1	cis	cerebellum	SCAN
rs11119340	TRAF3IP3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
3	chr1:209931000-209941800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:209931000-209942000	Weak transcription	Esophagus	oesophagus
5	chr1:209931000-209943200	Weak transcription	Lung	lung
6	chr1:209931000-209943600	Weak transcription	Gastric	stomach
7	chr1:209931800-209940600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:209932200-209941200	Genic enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:209932200-209941400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:209932200-209941800	Weak transcription	Colonic Mucosa	Colon
11	chr1:209932200-209942000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:209933000-209940800	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr1:209933400-209940600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:209933600-209940800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:209933800-209941600	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:209934000-209941600	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:209934600-209941600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:209934800-209940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:209934800-209941800	Weak transcription	Right Ventricle	heart
20	chr1:209934800-209942000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:209934800-209942000	Weak transcription	Right Atrium	heart
22	chr1:209935000-209940600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:209935200-209940600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:209936600-209940800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:209937000-209941600	Weak transcription	Spleen	Spleen
26	chr1:209937800-209940800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:209938200-209941000	Genic enhancers	Primary B cells from cord blood	blood
28	chr1:209938200-209941000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:209938800-209940600	Genic enhancers	Dnd41	blood
30	chr1:209938800-209940800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
31	chr1:209938800-209941400	Enhancers	Fetal Intestine Large	intestine
32	chr1:209939200-209940800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:209939200-209941000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:209939200-209941000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:209939200-209941000	Genic enhancers	Fetal Thymus	thymus
36	chr1:209939200-209941400	Genic enhancers	GM12878-XiMat	blood
37	chr1:209939200-209941600	Enhancers	Fetal Intestine Small	intestine
38	chr1:209939400-209940800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:209939400-209941400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr1:209939800-209941600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
41	chr1:209940000-209940600	Weak transcription	Thymus	Thymus
42	chr1:209940000-209940800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:209940000-209941200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:209940000-209941400	Enhancers	Primary hematopoietic stem cells	blood
45	chr1:209940000-209941400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:209940000-209941800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:209940200-209940800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr1:209940200-209941000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:209940200-209941000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:209940400-209941000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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