Variant report

Variant	rs12669549
Chromosome Location	chr7:21983259-21983260
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21920987..21923529-chr7:21981906..21983468,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10262937	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12700337	0.92[EUR][1000 genomes]
rs1534770	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823667	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4394298	0.88[EUR][1000 genomes]
rs55681513	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6461623	0.88[EUR][1000 genomes]
rs6946675	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9638794	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv870325	chr7:21979039-22120493	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12669549	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:21963600-21983600	Weak transcription	Ovary	ovary
4	chr7:21973200-21984200	Weak transcription	Esophagus	oesophagus
5	chr7:21976800-21984000	Weak transcription	Adipose Nuclei	Adipose
6	chr7:21977600-21983400	Weak transcription	Fetal Intestine Small	intestine
7	chr7:21978400-21984000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr7:21978600-21983400	Enhancers	Colon Smooth Muscle	Colon
9	chr7:21978600-21983400	Enhancers	HUVEC	blood vessel
10	chr7:21979200-21984000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr7:21979400-21984200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:21979800-21983600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:21979800-21984000	Weak transcription	Fetal Kidney	kidney
14	chr7:21980200-21984000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:21980400-21984000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:21980400-21984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:21980400-21984200	Weak transcription	Psoas Muscle	Psoas
18	chr7:21980800-21983400	Enhancers	NHDF-Ad	bronchial
19	chr7:21980800-21983600	Enhancers	Hela-S3	cervix
20	chr7:21980800-21983800	Enhancers	Rectal Smooth Muscle	rectum
21	chr7:21980800-21984000	Enhancers	Duodenum Mucosa	Duodenum
22	chr7:21981000-21983600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr7:21981000-21983800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr7:21981000-21984000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr7:21981000-21984000	Enhancers	Fetal Thymus	thymus
26	chr7:21981200-21983400	Enhancers	Right Ventricle	heart
27	chr7:21981200-21984000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr7:21981200-21984000	Enhancers	Fetal Lung	lung
29	chr7:21981400-21983400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:21981600-21983800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:21981600-21983800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr7:21981600-21984000	Weak transcription	HMEC	breast
33	chr7:21981600-21984200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:21981800-21983600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:21981800-21983600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr7:21981800-21983600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr7:21981800-21983600	Flanking Active TSS	Fetal Heart	heart
38	chr7:21981800-21984000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:21981800-21984000	Weak transcription	Right Atrium	heart
40	chr7:21982000-21983600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr7:21982000-21984000	Enhancers	Primary hematopoietic stem cells	blood
42	chr7:21982000-21984000	Enhancers	Fetal Stomach	stomach
43	chr7:21982200-21983400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:21982200-21984000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:21982400-21983400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
46	chr7:21982400-21983400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:21982400-21983400	Enhancers	Fetal Brain Female	brain
48	chr7:21982400-21983600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr7:21982400-21983600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr7:21982400-21984000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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