Variant report

Variant	rs11061881
Chromosome Location	chr12:1739836-1739837
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	SUZ12	chr12:1739328-1740832	NT2-D1	testis:	n/a	n/a
2	CTCF	chr12:1738798-1740032	SK-N-SH	brain:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
3	E2F6	chr12:1739384-1739983	A549	lung:	n/a	chr12:1739417-1739426
4	MAX	chr12:1739023-1740020	A549	lung:	n/a	chr12:1739601-1739611
5	NFIC	chr12:1739346-1739939	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr12:1738969-1739867	GM12878	blood:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
7	CTCF	chr12:1739014-1739843	MCF-7	breast:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
8	MAX	chr12:1739518-1740284	H1-hESC	embryonic stem cell:	n/a	chr12:1740060-1740069 chr12:1740059-1740066 chr12:1740058-1740067 chr12:1739601-1739611
9	MAX	chr12:1739425-1740006	A549	lung:	n/a	chr12:1739601-1739611
10	ZBTB7A	chr12:1738857-1739984	ECC-1	luminal epithelium:	n/a	chr12:1739440-1739448 chr12:1739416-1739425 chr12:1738964-1738978
11	CTCF	chr12:1739700-1739850	NB4	blood:	n/a	n/a
12	CTCF	chr12:1739740-1739890	HCM	heart:	n/a	n/a
13	MAX	chr12:1739417-1739930	MCF-7	breast:	n/a	chr12:1739601-1739611
14	CTCF	chr12:1739580-1739870	AG04450	lung:	n/a	chr12:1739583-1739596
15	EBF1	chr12:1739532-1739836	GM12878	blood:	n/a	n/a
16	CTCF	chr12:1739740-1739890	HA-sp	spinal cord:	n/a	n/a
17	ZBTB7A	chr12:1738734-1740013	ECC-1	luminal epithelium:	n/a	chr12:1739440-1739448 chr12:1739416-1739425 chr12:1738964-1738978
18	EP300	chr12:1737662-1740910	SK-N-SH	brain:	n/a	chr12:1740199-1740213 chr12:1739522-1739538 chr12:1739309-1739318
19	SUZ12	chr12:1739514-1740733	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr12:1739418-1739943	H1-hESC	embryonic stem cell:	n/a	chr12:1739601-1739611
21	GATA2	chr12:1737972-1739853	SH-SY5Y	brain:	n/a	chr12:1738891-1738899 chr12:1738889-1738902
22	SIN3A	chr12:1739038-1740735	H1-hESC	embryonic stem cell:	n/a	chr12:1739716-1739729
23	MAX	chr12:1739330-1740002	ECC-1	luminal epithelium:	n/a	chr12:1739601-1739611
24	E2F6	chr12:1739408-1740102	H1-hESC	embryonic stem cell:	n/a	chr12:1739417-1739426
25	CTCF	chr12:1739700-1739850	HCT-116	colon:	n/a	n/a
26	CTBP2	chr12:1738253-1739969	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr12:1739720-1739870	GM12867	blood:	n/a	n/a
28	MXI1	chr12:1737590-1740000	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:1739832-1739882	SK-N-MC	brain:	n/a
2	chr12:1739832-1739882	NH-A	brain:	n/a
3	chr12:1739832-1739882	GM12878	blood:	n/a
4	chr12:1739832-1739882	HCPEpiC	choroid plexus:	n/a
5	chr12:1739832-1739882	MCF-7	breast:	n/a
6	chr12:1739832-1739882	GM06990	blood:	n/a
7	chr12:1739832-1739882	HepG2	liver:	n/a
8	chr12:1739832-1739882	HEEpiC	esophagus:	n/a
9	chr12:1739832-1739882	NT2-D1	testis:	n/a
10	chr12:1739832-1739882	CMK	blood:	n/a
11	chr12:1739832-1739882	BE2_C	brain:	n/a
12	chr12:1739832-1739882	RPTEC	kidney:	n/a
13	chr12:1739832-1739882	AG09309	skin:	n/a
14	chr12:1739832-1739882	HMEC	breast:	n/a
15	chr12:1739832-1739882	HL-60	blood:	n/a
16	chr12:1739832-1739882	HIPEpiC	eye:	n/a
17	chr12:1739832-1739882	AG09319	gingival:	n/a
18	chr12:1739832-1739882	Hepatocyte	liver:	n/a
19	chr12:1739832-1739882	Jurkat	blood:	n/a
20	chr12:1739832-1739882	NB4	blood:	n/a
21	chr12:1739832-1739882	K562	blood:	n/a
22	chr12:1739832-1739882	PFSK-1	brain:	n/a
23	chr12:1739832-1739882	HEK293	kidney:	embryo
24	chr12:1739832-1739882	HRCEpiC	kidney:	n/a
25	chr12:1739832-1739882	IMR90	lung:	fetal
26	chr12:1739832-1739882	AG10803	skin:	n/a
27	chr12:1739832-1739882	H1-hESC	embryonic stem cell:	embryo
28	chr12:1739832-1739882	ECC-1	luminal epithelium:	n/a
29	chr12:1739832-1739882	HPAEpiC	pulmonary alveolar:	n/a
30	chr12:1739832-1739882	AG04450	lung:	fetal
31	chr12:1739832-1739882	HAEpiC	amniotic membrane:	n/a
32	chr12:1739832-1739882	HNPCEpiC	eye:	n/a
33	chr12:1739832-1739882	A549	lung:	n/a
34	chr12:1739832-1739882	LNCaP	prostate:	n/a
35	chr12:1739832-1739882	U87	brain:	n/a
36	chr12:1739832-1739882	MCF10A-Er-Src	breast:	n/a
37	chr12:1739832-1739882	PrEC	prostate:	n/a
38	chr12:1739832-1739882	AoSMC	blood vessel:	n/a
39	chr12:1739832-1739882	HUVEC	blood vessel:	n/a
40	chr12:1739832-1739882	GM12891	blood:	n/a
41	chr12:1739832-1739882	HCM	heart:	n/a
42	chr12:1739832-1739882	HCF	heart:	n/a
43	chr12:1739832-1739882	NHDF-neo	bronchial:	n/a
44	chr12:1739832-1739882	SKMC	muscle:	n/a
45	chr12:1739832-1739882	GM12892	blood:	n/a
46	chr12:1739832-1739882	HRE	kidney:	n/a
47	chr12:1739832-1739882	HRPEpiC	eye:	n/a
48	chr12:1739832-1739882	SK-N-SH_RA	brain:	n/a
49	chr12:1739832-1739882	NHBE	bronchial:	n/a
50	chr12:1739832-1739882	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1714212..1714749-chr12:1739345..1739945,2	MCF-7	breast:
2	chr12:1703157..1705505-chr12:1739226..1741204,2	MCF-7	breast:

Variant related genes	Relation type
WNT5B	TF binding region
WNT5B	CpG island
ENSG00000171823	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10773971	0.83[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061886	0.80[AMR][1000 genomes]
rs11061887	0.81[JPT][hapmap]
rs11061959	1.00[CEU][hapmap]
rs11061961	1.00[CEU][hapmap]
rs2270031	0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs2270034	1.00[ASW][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28384802	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7966046	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
8	nsv898587	chr12:1732295-1756642	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv898588	chr12:1736314-1755960	Bivalent Enhancer Enhancers Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv556994	chr12:1737309-1743843	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv898589	chr12:1738111-1755654	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11061881	SCGB2A2	trans	brain	seeQTL
rs11061881	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1733000-1744000	Weak transcription	K562	blood
2	chr12:1737600-1740600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:1737800-1740000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:1737800-1740400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr12:1737800-1740600	Enhancers	Spleen	Spleen
6	chr12:1737800-1740800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:1737800-1740800	Bivalent Enhancer	Fetal Lung	lung
8	chr12:1738000-1740000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:1738000-1740000	Enhancers	Fetal Brain Male	brain
10	chr12:1738000-1740000	Enhancers	Fetal Heart	heart
11	chr12:1738200-1740200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr12:1738200-1740400	Active TSS	Rectal Smooth Muscle	rectum
13	chr12:1738400-1740000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
14	chr12:1738400-1740400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:1738400-1740600	Enhancers	Lung	lung
16	chr12:1738600-1740000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:1738600-1740000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:1738600-1740000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:1738600-1740000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:1738600-1740000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:1738600-1740000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:1738600-1740200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:1738600-1740200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:1738600-1740200	Flanking Active TSS	Right Ventricle	heart
25	chr12:1738600-1740400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr12:1738600-1740600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:1738600-1740600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:1738600-1740600	Active TSS	Colon Smooth Muscle	Colon
29	chr12:1738600-1740800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr12:1738800-1740000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr12:1738800-1740000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:1738800-1740000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:1738800-1740000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:1738800-1740000	Active TSS	Brain Substantia Nigra	brain
35	chr12:1738800-1740200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:1738800-1740400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr12:1738800-1740400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:1738800-1740400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr12:1738800-1740600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr12:1738800-1740600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:1738800-1740600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr12:1739000-1740000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr12:1739000-1740000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
44	chr12:1739000-1740000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:1739000-1740000	Active TSS	Aorta	Aorta
46	chr12:1739000-1740000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:1739000-1740000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr12:1739000-1740000	Active TSS	Ovary	ovary
49	chr12:1739000-1740200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:1739000-1740200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood

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