Variant report

Variant	rs7167860
Chromosome Location	chr15:100016225-100016226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:100016174-100017645	SK-N-SH	brain:	n/a	chr15:100017358-100017368 chr15:100016826-100016835
2	JUND	chr15:100016159-100017485	SK-N-SH	brain:	n/a	chr15:100017208-100017218 chr15:100016826-100016837 chr15:100017359-100017368 chr15:100016828-100016836 chr15:100017208-100017218 chr15:100016590-100016602 chr15:100016826-100016838 chr15:100017209-100017217 chr15:100016869-100016880 chr15:100017205-100017216

No.	Distal block	Cell Line	Cell type
1	chr15:99969769..99972522-chr15:100015171..100016752,2	MCF-7	breast:
2	chr15:100010923..100013098-chr15:100015221..100016776,2	MCF-7	breast:
3	chr15:99991338..99992840-chr15:100014340..100017006,2	MCF-7	breast:
4	chr15:100013320..100017207-chr15:100104527..100106980,4	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region
ENSG00000259341	Chromatin interaction
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1020255	0.90[EUR][1000 genomes]
rs1020256	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10902545	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10902546	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10902547	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630522	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632243	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11632288	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632631	0.86[EUR][1000 genomes]
rs11633249	0.96[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs11637736	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903278	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904009	0.91[EUR][1000 genomes]
rs12909847	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1442645	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1867091	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867092	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867093	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1867094	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2119941	0.90[EUR][1000 genomes]
rs34457611	0.93[EUR][1000 genomes]
rs34666134	0.87[EUR][1000 genomes]
rs34974576	0.84[EUR][1000 genomes]
rs35015146	0.88[EUR][1000 genomes]
rs35395415	0.88[EUR][1000 genomes]
rs36112416	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4965251	0.89[EUR][1000 genomes]
rs56159751	0.89[EUR][1000 genomes]
rs56197704	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7172915	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180712	0.84[EUR][1000 genomes]
rs7181817	0.90[EUR][1000 genomes]
rs920657	0.84[CEU][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	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats 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	41 gene(s)	inside rSNPs	diseases
6	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
8	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
9	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1050527	chr15:99983054-100035436	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv17862	chr15:100015641-100016286	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7167860	MCTP2	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100008200-100020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:100008400-100016600	Weak transcription	Hela-S3	cervix
3	chr15:100012400-100018200	Enhancers	Stomach Mucosa	stomach
4	chr15:100012400-100018600	Enhancers	Spleen	Spleen
5	chr15:100012400-100018800	Enhancers	Right Atrium	heart
6	chr15:100012600-100018600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:100012600-100019000	Enhancers	Fetal Heart	heart
8	chr15:100012800-100018800	Enhancers	Fetal Lung	lung
9	chr15:100013000-100018600	Enhancers	Right Ventricle	heart
10	chr15:100013000-100018800	Enhancers	Fetal Muscle Trunk	muscle
11	chr15:100013000-100019400	Enhancers	Fetal Thymus	thymus
12	chr15:100013200-100019000	Enhancers	Fetal Muscle Leg	muscle
13	chr15:100013600-100016600	Enhancers	Stomach Smooth Muscle	stomach
14	chr15:100013600-100018400	Enhancers	Placenta	Placenta
15	chr15:100013600-100018400	Enhancers	Lung	lung
16	chr15:100013800-100016800	Enhancers	Adipose Nuclei	Adipose
17	chr15:100013800-100017000	Weak transcription	Gastric	stomach
18	chr15:100013800-100018200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:100013800-100018200	Enhancers	HMEC	breast
20	chr15:100014000-100017000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:100014000-100017000	Enhancers	HSMM	muscle
22	chr15:100014000-100018600	Enhancers	HSMMtube	muscle
23	chr15:100014000-100019200	Enhancers	Fetal Stomach	stomach
24	chr15:100014200-100016800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:100014400-100016400	Enhancers	Esophagus	oesophagus
26	chr15:100014400-100016800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:100014400-100017000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:100014400-100017000	Enhancers	NHLF	lung
29	chr15:100014600-100016400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr15:100014600-100017400	Enhancers	Colonic Mucosa	Colon
31	chr15:100014800-100016600	Weak transcription	GM12878-XiMat	blood
32	chr15:100014800-100016800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:100014800-100018800	Enhancers	Left Ventricle	heart
34	chr15:100014800-100020200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:100014800-100026800	Weak transcription	Aorta	Aorta
36	chr15:100015200-100017400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:100015200-100017600	Weak transcription	Fetal Kidney	kidney
38	chr15:100015200-100018600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:100015400-100016600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:100015400-100016600	Enhancers	HepG2	liver
41	chr15:100015400-100016800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr15:100015400-100016800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:100015400-100016800	Enhancers	Duodenum Mucosa	Duodenum
44	chr15:100015400-100017000	Enhancers	NHEK	skin
45	chr15:100015400-100018200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:100015400-100018400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr15:100015600-100016400	Enhancers	A549	lung
48	chr15:100015600-100016400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr15:100015600-100016600	Enhancers	Fetal Brain Female	brain
50	chr15:100015600-100016800	Enhancers	Primary T cells from cord blood	blood

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