Variant report

Variant	rs7521242
Chromosome Location	chr1:61803889-61803890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:61802472..61805415-chr1:61917120..61919669,2	MCF-7	breast:
2	chr1:61679578..61681382-chr1:61802246..61804281,2	MCF-7	breast:
3	chr1:61803556..61804528-chr1:61918731..61919655,3	MCF-7	breast:
4	chr1:61515264..61516149-chr1:61803341..61804328,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1041674	0.81[JPT][hapmap]
rs1125777	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2207787	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2364466	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364475	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2782540	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2806435	0.81[JPT][hapmap]
rs41350144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs6691768	0.82[JPT][hapmap]
rs7553528	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556462	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9436636	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7521242	MYSM1	cis	cerebellum	SCAN
rs7521242	MYSM1	cis	parietal	SCAN
rs7521242	PRSS21	trans	lymphoblastoid	seeQTL
rs7521242	RPS25	trans	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61786000-61813600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:61790000-61805400	Weak transcription	Lung	lung
3	chr1:61796200-61805400	Weak transcription	Esophagus	oesophagus
4	chr1:61798600-61805000	Enhancers	Fetal Heart	heart
5	chr1:61800200-61804400	Enhancers	Brain Germinal Matrix	brain
6	chr1:61800400-61804000	Enhancers	Liver	Liver
7	chr1:61801000-61805400	Weak transcription	Pancreas	Pancrea
8	chr1:61801000-61818600	Weak transcription	K562	blood
9	chr1:61801200-61824600	Weak transcription	Gastric	stomach
10	chr1:61802200-61804400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:61802200-61804400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:61802200-61804400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:61802200-61804600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:61802200-61804800	Enhancers	Fetal Stomach	stomach
15	chr1:61802200-61805000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:61802200-61805200	Enhancers	Fetal Lung	lung
17	chr1:61802200-61805800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:61802400-61804000	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:61802400-61804000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:61802400-61804000	Enhancers	Fetal Intestine Large	intestine
21	chr1:61802400-61804200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:61802400-61804200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:61802400-61804400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:61802400-61804400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:61802400-61804400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:61802400-61804400	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:61802600-61804000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:61802600-61804000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:61802600-61804200	Enhancers	Fetal Muscle Leg	muscle
30	chr1:61802600-61804400	Enhancers	Colon Smooth Muscle	Colon
31	chr1:61802600-61804600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:61802800-61804000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:61802800-61804000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:61802800-61804000	Enhancers	Right Ventricle	heart
35	chr1:61802800-61804200	Bivalent Enhancer	NH-A	brain
36	chr1:61802800-61804400	Enhancers	Placenta	Placenta
37	chr1:61802800-61804400	Enhancers	Ovary	ovary
38	chr1:61802800-61804600	Enhancers	Brain Angular Gyrus	brain
39	chr1:61802800-61804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:61802800-61804600	Enhancers	Fetal Kidney	kidney
41	chr1:61803000-61805000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:61803000-61816200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:61803200-61804000	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:61803200-61804000	Flanking Active TSS	Osteobl	bone
45	chr1:61803200-61804200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr1:61803400-61804000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:61803400-61804000	Enhancers	Stomach Mucosa	stomach
48	chr1:61803400-61804200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:61803400-61804200	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr1:61803400-61804600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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