Variant report

Variant	rs12666447
Chromosome Location	chr7:27937267-27937268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27936636..27940623-chr7:27942043..27944252,3	MCF-7	breast:
2	chr7:27928475..27932092-chr7:27934786..27940167,5	K562	blood:
3	chr7:27933855..27936003-chr7:27936219..27938818,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10267854	1.00[LWK][hapmap]
rs10452749	0.85[MEX][hapmap]
rs1055445	0.96[ASN][1000 genomes]
rs12535525	0.93[ASN][1000 genomes]
rs12666442	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12668668	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs17621310	0.96[ASN][1000 genomes]
rs189	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs193	0.81[CHD][hapmap]
rs194	0.81[CHD][hapmap]
rs2040668	0.85[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs220	0.95[ASN][1000 genomes]
rs4719914	0.81[CHD][hapmap]
rs62451112	0.88[EUR][1000 genomes]
rs62451116	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62451117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72598551	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72598552	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757136	1.00[LWK][hapmap]
rs7784038	1.00[LWK][hapmap]
rs9791862	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12666447	CYCS	cis	parietal	SCAN
rs12666447	CRHR2	cis	parietal	SCAN
rs12666447	HOXA13	cis	parietal	SCAN
rs12666447	TRIL	cis	cerebellum	SCAN
rs12666447	SNX10	cis	cerebellum	SCAN
rs12666447	TRIL	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27915400-27939400	Weak transcription	NHDF-Ad	bronchial
2	chr7:27923800-27941000	Weak transcription	Fetal Brain Female	brain
3	chr7:27924000-27938800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:27924000-27938800	Weak transcription	Spleen	Spleen
5	chr7:27926600-27956000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:27928000-27939800	Weak transcription	Osteobl	bone
7	chr7:27928400-27940600	Weak transcription	NHLF	lung
8	chr7:27928400-27940800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:27928800-27937400	Weak transcription	Psoas Muscle	Psoas
10	chr7:27930000-27938400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:27930000-27939600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:27930000-27949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:27930800-27939600	Weak transcription	GM12878-XiMat	blood
14	chr7:27931200-27939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:27931600-27939400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:27931800-27938800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:27931800-27940800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:27931800-27941000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:27932000-27941000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:27932800-27941000	Weak transcription	Thymus	Thymus
21	chr7:27933600-27938400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:27934000-27939600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:27934000-27940600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:27934200-27938400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:27934200-27938600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:27934200-27939400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:27934200-27940000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:27934200-27940200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:27934400-27937400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:27934400-27938200	Weak transcription	Ovary	ovary
31	chr7:27934400-27938400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:27934400-27939400	Weak transcription	Adipose Nuclei	Adipose
33	chr7:27934400-27940800	Weak transcription	Aorta	Aorta
34	chr7:27934400-27940800	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:27934400-27940800	Weak transcription	Fetal Stomach	stomach
36	chr7:27934400-27940800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:27934600-27941000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:27934600-27941000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:27935000-27937400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:27935000-27937600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:27935200-27937400	Enhancers	Colon Smooth Muscle	Colon
42	chr7:27935200-27939800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:27935400-27937400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr7:27935400-27939000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:27935600-27943200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:27935800-27937400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr7:27935800-27938200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr7:27935800-27938200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr7:27935800-27938200	Weak transcription	Primary T cells from cord blood	blood
50	chr7:27935800-27938200	Weak transcription	Fetal Thymus	thymus

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