Variant report

Variant	rs11061980
Chromosome Location	chr12:1888248-1888249
allele	A/C
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	CTCF	chr12:1888183-1888272	Lung_OC	lung:	n/a	n/a
2	CTCF	chr12:1888100-1888250	HMF	breast:	n/a	n/a
3	STAT3	chr12:1888135-1888476	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:1888135-1888482	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:1888134-1888473	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr12:1888135-1888469	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr12:1888201-1888401	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr12:1888073-1888489	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1881087..1883067-chr12:1886344..1888819,2	K562	blood:

Variant related genes	Relation type
ADIPOR2	TF binding region
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10491959	1.00[YRI][hapmap]
rs11061928	1.00[YRI][hapmap]
rs11061929	1.00[YRI][hapmap]
rs11061931	1.00[YRI][hapmap]
rs11061932	1.00[YRI][hapmap]
rs11061958	1.00[YRI][hapmap]
rs11061961	1.00[YRI][hapmap]
rs11061979	1.00[YRI][hapmap]
rs11613594	1.00[YRI][hapmap]
rs11614622	1.00[YRI][hapmap]
rs12230994	1.00[YRI][hapmap]
rs16928662	1.00[YRI][hapmap]
rs16928665	1.00[YRI][hapmap]
rs2041139	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2286382	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1038425	chr12:1857052-1902302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
2	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
3	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
4	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
7	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:1867200-1892600	Weak transcription	Spleen	Spleen
9	chr12:1867200-1893000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:1868200-1901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:1870200-1892600	Weak transcription	Ovary	ovary
12	chr12:1878600-1897800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:1879000-1904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:1880600-1888400	Weak transcription	Fetal Stomach	stomach
15	chr12:1880600-1892200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:1880600-1892200	Weak transcription	Gastric	stomach
17	chr12:1880600-1892200	Weak transcription	Lung	lung
18	chr12:1880600-1894600	Weak transcription	Esophagus	oesophagus
19	chr12:1881200-1889000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:1881600-1897400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:1881600-1897600	Strong transcription	Dnd41	blood
22	chr12:1881600-1897800	Strong transcription	Fetal Thymus	thymus
23	chr12:1882000-1889000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:1882000-1898200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:1882400-1893000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:1882400-1896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:1882600-1888400	Weak transcription	Fetal Lung	lung
28	chr12:1882600-1889000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:1882600-1904800	Weak transcription	Stomach Mucosa	stomach
30	chr12:1883200-1889200	Enhancers	NHDF-Ad	bronchial
31	chr12:1883200-1889600	Weak transcription	Placenta	Placenta
32	chr12:1883400-1889200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:1883400-1890000	Enhancers	Brain Anterior Caudate	brain
34	chr12:1883800-1888800	Weak transcription	Brain Germinal Matrix	brain
35	chr12:1885000-1888400	Strong transcription	HepG2	liver
36	chr12:1885200-1888400	Strong transcription	GM12878-XiMat	blood
37	chr12:1885200-1889600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:1885200-1904600	Weak transcription	Fetal Brain Male	brain
39	chr12:1885400-1892200	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:1885400-1897800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:1885400-1898000	Strong transcription	Primary T cells from cord blood	blood
42	chr12:1885600-1895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:1885600-1897600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr12:1885600-1902600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:1885800-1889600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:1885800-1890600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:1885800-1896600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:1885800-1904000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:1886000-1888400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:1886000-1888400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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