Variant report

Variant	rs13109291
Chromosome Location	chr4:7808752-7808753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7808655..7810334-chr4:7810904..7813896,2	MCF-7	breast:
2	chr4:7807434..7808952-chr4:8000439..8002438,2	MCF-7	breast:
3	chr4:7803065..7804892-chr4:7807691..7809470,2	K562	blood:
4	chr4:7803065..7805141-chr4:7807691..7809396,2	K562	blood:
5	chr4:7806783..7809609-chr4:7939273..7941651,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10029941	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557817	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2018399	0.82[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2107182	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs28475763	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4388087	0.85[CHB][hapmap]
rs4404542	0.85[CHB][hapmap]
rs4413405	0.85[CHB][hapmap]
rs4689867	0.88[ASN][1000 genomes]
rs60840998	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446619	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6827395	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6828807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6829473	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6838291	0.82[CHB][hapmap]
rs6852990	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs756255	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active 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	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	esv2763337	chr4:7807183-7811303	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13109291	CRMP1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
3	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:7802400-7812400	Weak transcription	Spleen	Spleen
8	chr4:7802600-7809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:7802600-7810400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:7802800-7809400	Weak transcription	Esophagus	oesophagus
11	chr4:7803000-7812400	Weak transcription	Colonic Mucosa	Colon
12	chr4:7803800-7809200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:7803800-7810200	Enhancers	Fetal Heart	heart
14	chr4:7804000-7829200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:7804600-7809400	Genic enhancers	Osteobl	bone
16	chr4:7805200-7809600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:7805200-7822600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:7805400-7809600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:7805600-7809600	Enhancers	Colon Smooth Muscle	Colon
20	chr4:7805600-7809800	Enhancers	Brain Hippocampus Middle	brain
21	chr4:7805600-7810400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:7805600-7816400	Genic enhancers	Fetal Stomach	stomach
23	chr4:7805800-7809400	Enhancers	Fetal Muscle Trunk	muscle
24	chr4:7805800-7809600	Enhancers	Stomach Mucosa	stomach
25	chr4:7805800-7810600	Enhancers	Ovary	ovary
26	chr4:7806000-7808800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:7806000-7809000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:7806000-7809200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:7806000-7810000	Enhancers	Fetal Kidney	kidney
30	chr4:7806000-7810200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr4:7806000-7814000	Enhancers	Adipose Nuclei	Adipose
32	chr4:7806200-7808800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:7806200-7809000	Genic enhancers	NH-A	brain
34	chr4:7806200-7809600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:7806200-7809800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:7806200-7810000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:7806200-7819200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:7806400-7809400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:7806400-7809400	Genic enhancers	Fetal Intestine Large	intestine
40	chr4:7806400-7809600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:7806400-7824600	Weak transcription	Fetal Thymus	thymus
42	chr4:7806600-7809400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:7806600-7809600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:7806600-7809600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:7806600-7809600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:7806600-7809800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr4:7806600-7810000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:7806800-7808800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr4:7806800-7809600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:7806800-7809600	Enhancers	Brain Germinal Matrix	brain

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