Variant report

Variant	rs55681513
Chromosome Location	chr7:21979511-21979512
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21976274..21979675-chr7:21983626..21985633,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164649	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10262937	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12669549	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700337	0.87[EUR][1000 genomes]
rs1534770	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3823667	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4394298	0.89[EUR][1000 genomes]
rs6461623	0.89[EUR][1000 genomes]
rs6946675	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9638794	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv275068	chr7:21966107-21980773	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
rs55681513	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:21951600-21982600	Weak transcription	HSMM	muscle
4	chr7:21955000-21979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:21955000-21981000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:21956000-21981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:21956400-21980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:21963600-21983600	Weak transcription	Ovary	ovary
10	chr7:21965200-21982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:21966600-21981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:21967800-21979600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:21967800-21982000	Weak transcription	Fetal Stomach	stomach
14	chr7:21973200-21981200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr7:21973200-21984200	Weak transcription	Esophagus	oesophagus
16	chr7:21974800-21981000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:21975800-21980600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:21975800-21982600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:21976200-21979600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:21976200-21982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:21976400-21982400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:21976800-21984000	Weak transcription	Adipose Nuclei	Adipose
23	chr7:21977200-21982400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:21977400-21980600	Genic enhancers	Primary B cells from cord blood	blood
25	chr7:21977600-21980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:21977600-21983400	Weak transcription	Fetal Intestine Small	intestine
27	chr7:21977800-21980400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:21978000-21980200	Flanking Active TSS	GM12878-XiMat	blood
29	chr7:21978200-21979800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:21978200-21980800	Weak transcription	NHDF-Ad	bronchial
31	chr7:21978400-21979800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:21978400-21980400	Enhancers	Left Ventricle	heart
33	chr7:21978400-21980400	Enhancers	Psoas Muscle	Psoas
34	chr7:21978400-21982400	Enhancers	Primary B cells from peripheral blood	blood
35	chr7:21978400-21984000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr7:21978600-21979800	Enhancers	Primary hematopoietic stem cells	blood
37	chr7:21978600-21980400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr7:21978600-21981800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr7:21978600-21983400	Enhancers	Colon Smooth Muscle	Colon
40	chr7:21978600-21983400	Enhancers	HUVEC	blood vessel
41	chr7:21978800-21979600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr7:21978800-21979600	Enhancers	Stomach Smooth Muscle	stomach
43	chr7:21978800-21979800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr7:21978800-21979800	Enhancers	Fetal Kidney	kidney
45	chr7:21978800-21979800	Enhancers	Fetal Lung	lung
46	chr7:21978800-21980000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
47	chr7:21978800-21980200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:21978800-21981200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:21978800-21981200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:21978800-21982800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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