Variant report

Variant	rs12148825
Chromosome Location	chr15:99846612-99846613
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99845791..99847734-chr15:99849228..99852501,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13853	0.83[CHD][hapmap]
rs1510059	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2136628	0.81[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289558	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs260086	0.83[CHD][hapmap]
rs2602037	0.85[CHD][hapmap]
rs28651946	0.86[EUR][1000 genomes]
rs28729666	0.85[EUR][1000 genomes]
rs4640164	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030691	0.83[CHD][hapmap]
rs58762669	0.85[EUR][1000 genomes]
rs59136665	0.86[EUR][1000 genomes]
rs59855164	0.85[EUR][1000 genomes]
rs62023803	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62023804	0.91[ASN][1000 genomes]
rs62023806	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023807	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023809	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023810	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023811	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023845	0.91[ASN][1000 genomes]
rs62023846	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62023847	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62023852	0.86[EUR][1000 genomes]
rs62023854	0.86[EUR][1000 genomes]
rs62023857	0.85[EUR][1000 genomes]
rs62023858	0.85[EUR][1000 genomes]
rs62025360	0.85[EUR][1000 genomes]
rs62025361	0.85[EUR][1000 genomes]
rs62025363	0.85[EUR][1000 genomes]
rs62025364	0.84[EUR][1000 genomes]
rs62025365	0.85[EUR][1000 genomes]
rs62025695	0.81[ASN][1000 genomes]
rs6422002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167033	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169075	1.00[MEX][hapmap]
rs7170268	0.83[CHD][hapmap]
rs7172305	1.00[MEX][hapmap]
rs7181876	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181973	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs768159	1.00[CHB][hapmap]
rs8032790	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039637	1.00[CHD][hapmap]
rs8041236	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs978703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	60 gene(s)	inside rSNPs	diseases
4	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
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	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
9	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
10	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking 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	31 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	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
15	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	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
17	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
18	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
19	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
20	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12148825	SYNM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
2	chr15:99793000-99850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:99793000-99866600	Weak transcription	Gastric	stomach
4	chr15:99794200-99847000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:99819800-99854800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:99824000-99847000	Weak transcription	Spleen	Spleen
7	chr15:99829600-99847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:99831400-99848800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:99832600-99846800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
11	chr15:99834200-99851800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:99835200-99846800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:99835200-99851200	Weak transcription	Primary B cells from cord blood	blood
14	chr15:99835200-99864200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:99835400-99850000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:99835400-99852600	Weak transcription	Fetal Intestine Large	intestine
17	chr15:99836400-99852400	Weak transcription	Fetal Thymus	thymus
18	chr15:99836600-99847000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:99836800-99852200	Weak transcription	Dnd41	blood
20	chr15:99837200-99851200	Weak transcription	Primary T cells from cord blood	blood
21	chr15:99838600-99847000	Weak transcription	Esophagus	oesophagus
22	chr15:99843000-99847400	Enhancers	Liver	Liver
23	chr15:99843400-99848400	Enhancers	Fetal Lung	lung
24	chr15:99844000-99846800	Enhancers	Fetal Heart	heart
25	chr15:99844400-99846800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:99845200-99848400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:99845200-99849200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr15:99845400-99846800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:99845400-99847000	Weak transcription	Left Ventricle	heart
30	chr15:99845400-99848200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr15:99845600-99848200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr15:99845800-99846800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:99845800-99846800	Enhancers	HSMMtube	muscle
34	chr15:99845800-99847600	Enhancers	Fetal Stomach	stomach
35	chr15:99846000-99846800	Enhancers	NH-A	brain
36	chr15:99846000-99847000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:99846000-99847200	Enhancers	NHLF	lung
38	chr15:99846000-99847400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:99846000-99847400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:99846000-99847400	Flanking Active TSS	A549	lung
41	chr15:99846000-99847600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr15:99846000-99847600	Enhancers	HMEC	breast
43	chr15:99846000-99847600	Enhancers	HSMM	muscle
44	chr15:99846000-99847800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:99846000-99847800	Enhancers	Osteobl	bone
46	chr15:99846000-99848000	Enhancers	Fetal Kidney	kidney
47	chr15:99846000-99848400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr15:99846200-99846800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:99846200-99846800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:99846200-99846800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links