Variant report

Variant	rs11038871
Chromosome Location	chr11:46379442-46379443
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	MAX	chr11:46378799-46379632	ECC-1	luminal epithelium:	n/a	chr11:46379058-46379068
2	TEAD4	chr11:46378880-46379551	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr11:46378849-46379495	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr11:46378371-46379767	HL-60	blood:	n/a	n/a
5	TEAD4	chr11:46378862-46379519	ECC-1	luminal epithelium:	n/a	n/a
6	HMGN3	chr11:46379139-46379453	K562	blood:	n/a	n/a
7	POLR2A	chr11:46378903-46379651	K562	blood:	n/a	n/a
8	TCF12	chr11:46378897-46379598	ECC-1	luminal epithelium:	n/a	chr11:46379032-46379039 chr11:46379419-46379426 chr11:46378931-46378938
9	NFIC	chr11:46378899-46379558	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr11:46378422-46379730	HL-60	blood:	n/a	n/a
11	ZNF143	chr11:46379144-46379446	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:46379120-46379489	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr11:46377956-46379690	NB4	blood:	n/a	chr11:46378164-46378173 chr11:46378163-46378174 chr11:46378164-46378173 chr11:46378163-46378173 chr11:46379058-46379068 chr11:46378163-46378174 chr11:46378164-46378173 chr11:46378163-46378173 chr11:46378162-46378175 chr11:46378163-46378174
14	MYC	chr11:46378188-46379521	NB4	blood:	n/a	chr11:46379058-46379068
15	MAX	chr11:46378841-46379567	ECC-1	luminal epithelium:	n/a	chr11:46379058-46379068
16	TCF12	chr11:46378875-46379696	ECC-1	luminal epithelium:	n/a	chr11:46379032-46379039 chr11:46379419-46379426 chr11:46378931-46378938

No.	Distal block	Cell Line	Cell type
1	chr11:46378579..46380174-chr11:46393901..46396328,2	MCF-7	breast:
2	chr11:46266732..46269706-chr11:46378286..46381053,3	MCF-7	breast:
3	chr11:46379173..46381825-chr11:46695646..46697480,2	MCF-7	breast:
4	chr11:46367270..46371299-chr11:46374022..46379881,6	MCF-7	breast:

Variant related genes	Relation type
DGKZ	TF binding region
ENSG00000149091	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10838596	0.88[CEU][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs10838601	0.85[EUR][1000 genomes]
rs11038866	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11038910	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs12273290	0.84[AMR][1000 genomes]
rs1317826	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17787804	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3740973	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3802890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4565870	0.88[AMR][1000 genomes]
rs6485686	0.80[EUR][1000 genomes]
rs7476	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs7484125	0.86[EUR][1000 genomes]
rs7925678	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs7949282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs7949371	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1797501	chr11:46315437-46402521	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv1811345	chr11:46317062-46438072	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv897316	chr11:46349631-46417815	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv897317	chr11:46363411-46417815	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immunoglobulin A	20694011	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11038871	OR4X2	cis	parietal	SCAN
rs11038871	ACP2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46370000-46384000	Weak transcription	Fetal Kidney	kidney
2	chr11:46370000-46395800	Weak transcription	Aorta	Aorta
3	chr11:46370400-46382400	Weak transcription	Psoas Muscle	Psoas
4	chr11:46370400-46384000	Weak transcription	A549	lung
5	chr11:46370600-46382600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:46370800-46382400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:46370800-46382600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:46370800-46382800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:46371000-46382400	Weak transcription	HSMMtube	muscle
10	chr11:46371000-46382400	Weak transcription	HUVEC	blood vessel
11	chr11:46371400-46380200	Genic enhancers	Fetal Thymus	thymus
12	chr11:46371400-46382400	Weak transcription	NH-A	brain
13	chr11:46372600-46381600	Weak transcription	Hela-S3	cervix
14	chr11:46373800-46382600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:46374000-46382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:46374000-46382400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:46374200-46382600	Weak transcription	Fetal Intestine Large	intestine
18	chr11:46374200-46384400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:46374400-46379600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:46374400-46389600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:46374400-46389600	Weak transcription	Fetal Brain Female	brain
22	chr11:46374600-46380000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:46374600-46382400	Weak transcription	Liver	Liver
24	chr11:46374600-46382600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:46374800-46380000	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr11:46375000-46382400	Weak transcription	Fetal Heart	heart
27	chr11:46375200-46382200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:46375200-46382400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:46375400-46382400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:46375400-46382400	Weak transcription	Brain Anterior Caudate	brain
31	chr11:46375400-46382400	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:46375400-46382400	Weak transcription	NHLF	lung
33	chr11:46375600-46379600	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr11:46375600-46382200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:46375600-46382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:46375800-46382400	Weak transcription	Fetal Lung	lung
37	chr11:46375800-46382600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:46376000-46389600	Weak transcription	Brain Germinal Matrix	brain
39	chr11:46376200-46379800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr11:46376400-46380200	Genic enhancers	Primary T cells from cord blood	blood
41	chr11:46377000-46379800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:46377600-46379600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:46377800-46379600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:46377800-46379800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:46377800-46379800	Enhancers	Pancreas	Pancrea
46	chr11:46377800-46380200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:46378000-46379600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr11:46378000-46379600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr11:46378200-46379600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:46378200-46379600	Enhancers	Primary hematopoietic stem cells	blood

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