Variant report

Variant	rs7538419
Chromosome Location	chr1:45136475-45136476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45135137..45136656-chr1:45184445..45187267,2	MCF-7	breast:
2	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
3	chr1:45135067..45137597-chr1:45138521..45141291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187147	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000126106	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11581074	0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs11582807	0.96[ASN][1000 genomes]
rs11588956	0.88[CHD][hapmap]
rs12022097	0.85[ASN][1000 genomes]
rs1276066	0.85[AMR][1000 genomes]
rs1963490	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236219	0.84[CHD][hapmap]
rs34948326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850853	0.88[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4660818	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs4660821	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4660822	0.96[ASN][1000 genomes]
rs6429544	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs6667593	0.86[CHB][hapmap];0.96[YRI][hapmap]
rs6668870	0.96[ASN][1000 genomes]
rs6683133	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539607	0.90[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7538419	DMAP1	cis	parietal	SCAN
rs7538419	TM6SF1	trans	parietal	SCAN
rs7538419	MUTYH	cis	parietal	SCAN
rs7538419	ZNF684	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
2	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
4	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
6	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
7	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:45119800-45138000	Weak transcription	Primary T cells from cord blood	blood
10	chr1:45121000-45137600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45121000-45138600	Weak transcription	Gastric	stomach
12	chr1:45125400-45137800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:45125400-45138000	Weak transcription	Fetal Brain Female	brain
14	chr1:45126200-45136800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:45126200-45137600	Weak transcription	Adipose Nuclei	Adipose
16	chr1:45126200-45137800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:45126400-45137600	Weak transcription	Fetal Stomach	stomach
18	chr1:45126400-45137800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:45126400-45138200	Weak transcription	Fetal Lung	lung
20	chr1:45127800-45138400	Weak transcription	Small Intestine	intestine
21	chr1:45128200-45137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:45128200-45137600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:45128400-45136800	Weak transcription	Placenta	Placenta
24	chr1:45128400-45137600	Weak transcription	Right Atrium	heart
25	chr1:45128400-45137800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:45128600-45136800	Weak transcription	Brain Anterior Caudate	brain
27	chr1:45128600-45137000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:45128600-45137800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:45128600-45138000	Weak transcription	Ovary	ovary
30	chr1:45128800-45137600	Weak transcription	Liver	Liver
31	chr1:45128800-45137600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:45128800-45138000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:45129400-45138200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:45129600-45138000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:45129600-45138000	Weak transcription	HepG2	liver
36	chr1:45130600-45137600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:45130800-45136600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:45130800-45137000	Weak transcription	Lung	lung
39	chr1:45130800-45138000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:45130800-45139000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:45130800-45139000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:45131000-45136800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:45131000-45137000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:45131000-45137600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:45131200-45136800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:45132600-45138000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:45132600-45138000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:45134400-45137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:45134600-45137000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:45135000-45137200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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