Variant report

Variant	rs12700337
Chromosome Location	chr7:21981938-21981939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21980188..21982336-chr7:21983683..21985760,3	MCF-7	breast:
2	chr7:21920987..21923529-chr7:21981906..21983468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164649	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10262937	0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12669549	0.92[EUR][1000 genomes]
rs3823667	0.81[EUR][1000 genomes]
rs4394298	0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55681513	0.87[EUR][1000 genomes]
rs6461623	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946675	0.97[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7807075	0.82[CHB][hapmap]
rs9638794	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
rs12700337	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr7:21951600-21982600	Weak transcription	HSMM	muscle
3	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:21963600-21983600	Weak transcription	Ovary	ovary
5	chr7:21965200-21982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:21967800-21982000	Weak transcription	Fetal Stomach	stomach
7	chr7:21973200-21984200	Weak transcription	Esophagus	oesophagus
8	chr7:21975800-21982600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr7:21976200-21982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:21976400-21982400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:21976800-21984000	Weak transcription	Adipose Nuclei	Adipose
12	chr7:21977200-21982400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:21977600-21983400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:21978400-21982400	Enhancers	Primary B cells from peripheral blood	blood
15	chr7:21978400-21984000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr7:21978600-21983400	Enhancers	Colon Smooth Muscle	Colon
17	chr7:21978600-21983400	Enhancers	HUVEC	blood vessel
18	chr7:21978800-21982800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:21979200-21983200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr7:21979200-21984000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr7:21979400-21982800	Weak transcription	HSMMtube	muscle
22	chr7:21979400-21983000	Weak transcription	NHLF	lung
23	chr7:21979400-21984200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:21979600-21982600	Weak transcription	NH-A	brain
25	chr7:21979800-21982600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:21979800-21983600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:21979800-21984000	Weak transcription	Fetal Kidney	kidney
28	chr7:21980200-21984000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:21980400-21982400	Enhancers	Brain Anterior Caudate	brain
30	chr7:21980400-21982400	Enhancers	Stomach Smooth Muscle	stomach
31	chr7:21980400-21982600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:21980400-21982600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:21980400-21982600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr7:21980400-21982600	Weak transcription	Lung	lung
35	chr7:21980400-21984000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:21980400-21984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:21980400-21984200	Weak transcription	Psoas Muscle	Psoas
38	chr7:21980600-21982200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr7:21980800-21982200	Flanking Active TSS	GM12878-XiMat	blood
40	chr7:21980800-21982600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:21980800-21982600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr7:21980800-21983400	Enhancers	NHDF-Ad	bronchial
43	chr7:21980800-21983600	Enhancers	Hela-S3	cervix
44	chr7:21980800-21983800	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:21980800-21984000	Enhancers	Duodenum Mucosa	Duodenum
46	chr7:21981000-21982000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr7:21981000-21982000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:21981000-21982000	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr7:21981000-21982000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr7:21981000-21982400	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links