Variant report

Variant	rs7932404
Chromosome Location	chr11:3888234-3888235
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	FOXA1	chr11:3887988-3888595	HepG2	liver:	n/a	n/a
2	CUX1	chr11:3888149-3888291	GM12878	blood:	n/a	n/a
3	NR2F2	chr11:3887963-3889677	K562	blood:	n/a	chr11:3889425-3889440
4	JUN	chr11:3888049-3888476	HepG2	liver:	n/a	chr11:3888081-3888093
5	JUND	chr11:3888179-3888524	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:3888149-3888297	MCF10A-Er-Src	breast:	n/a	n/a
7	FOXA1	chr11:3888097-3888687	HepG2	liver:	n/a	n/a
8	FOXA1	chr11:3888106-3888678	HepG2	liver:	n/a	n/a
9	TBL1XR1	chr11:3888157-3888818	GM12878	blood:	n/a	n/a
10	ARID3A	chr11:3888130-3888624	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10835217	0.85[ASN][1000 genomes]
rs10835262	0.85[GIH][hapmap]
rs11030122	0.85[ASN][1000 genomes]
rs11030128	0.94[ASN][1000 genomes]
rs12275981	0.82[ASN][1000 genomes]
rs1869084	0.85[GIH][hapmap]
rs1869085	0.85[GIH][hapmap]
rs4414209	0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4910582	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7126252	0.93[ASN][1000 genomes]
rs7126870	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7952083	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv896894	chr11:3859856-3888234	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7932404	KL	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3881000-3888400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:3881200-3888400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr11:3881200-3888600	Weak transcription	Ovary	ovary
4	chr11:3882600-3889400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr11:3882800-3888800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:3883000-3893200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:3883000-3893400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:3883200-3889400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:3883200-3890200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr11:3883200-3893600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:3883400-3888600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:3883800-3893600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:3883800-3893800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:3884400-3888600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:3884600-3889200	Enhancers	Spleen	Spleen
16	chr11:3884600-3889400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:3884600-3889800	Enhancers	Primary B cells from peripheral blood	blood
18	chr11:3884600-3890200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:3884800-3889000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:3884800-3889400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:3884800-3889600	Enhancers	Colon Smooth Muscle	Colon
22	chr11:3885000-3888400	Enhancers	Liver	Liver
23	chr11:3885200-3888600	Enhancers	Rectal Smooth Muscle	rectum
24	chr11:3885200-3889600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr11:3885200-3889800	Enhancers	Adipose Nuclei	Adipose
26	chr11:3885200-3889800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr11:3885400-3889600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:3885400-3889600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr11:3885400-3889800	Enhancers	Small Intestine	intestine
30	chr11:3885600-3889400	Enhancers	Left Ventricle	heart
31	chr11:3885600-3889400	Flanking Active TSS	GM12878-XiMat	blood
32	chr11:3885600-3889800	Enhancers	Fetal Muscle Leg	muscle
33	chr11:3885600-3889800	Enhancers	Fetal Thymus	thymus
34	chr11:3885800-3889200	Enhancers	Aorta	Aorta
35	chr11:3885800-3889400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:3885800-3889600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:3886000-3889200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:3886000-3889400	Enhancers	HMEC	breast
39	chr11:3886000-3889600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:3886000-3889800	Enhancers	NHEK	skin
41	chr11:3886200-3889400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr11:3886200-3889400	Enhancers	NHDF-Ad	bronchial
43	chr11:3886200-3890400	Enhancers	Fetal Heart	heart
44	chr11:3886400-3889600	Enhancers	Fetal Lung	lung
45	chr11:3886400-3890200	Enhancers	Stomach Mucosa	stomach
46	chr11:3886400-3893600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr11:3886600-3888600	Enhancers	A549	lung
48	chr11:3886600-3888800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr11:3886600-3889400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:3886600-3889400	Enhancers	Colonic Mucosa	Colon

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