Variant report

Variant	rs7167899
Chromosome Location	chr15:99850880-99850881
allele	A/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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MEF2A-7	chr15:99848897-99851046	l_1246_chr15:99847899-99851046_liver

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1033035	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1033036	0.85[CEU][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10902543	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10902544	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11247079	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11247080	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs11247081	0.86[ASN][1000 genomes]
rs11853278	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12592075	0.87[JPT][hapmap]
rs12911768	0.96[YRI][hapmap]
rs12912927	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12913897	0.80[CHD][hapmap];0.87[JPT][hapmap]
rs1472989	0.86[ASN][1000 genomes]
rs1812344	0.87[ASN][1000 genomes]
rs1876927	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2048305	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2175225	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28520505	0.82[ASN][1000 genomes]
rs2862139	0.91[YRI][hapmap]
rs28807370	0.84[MEX][hapmap]
rs3851679	0.85[ASN][1000 genomes]
rs3863401	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6598237	0.82[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7167119	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7167542	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7168227	0.82[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7169906	0.85[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7171970	0.81[ASN][1000 genomes]
rs7173844	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182425	0.82[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7182675	0.87[JPT][hapmap]
rs7498053	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8036160	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs8038970	0.81[EUR][1000 genomes]
rs8040850	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8041923	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8042021	0.86[YRI][hapmap]
rs8042249	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8042667	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7167899	C15orf51	cis	cerebellum	SCAN
rs7167899	TTC23	cis	cerebellum	SCAN
rs7167899	LRRK1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99793000-99866600	Weak transcription	Gastric	stomach
2	chr15:99819800-99854800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
4	chr15:99834200-99851800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:99835200-99851200	Weak transcription	Primary B cells from cord blood	blood
6	chr15:99835200-99864200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:99835400-99852600	Weak transcription	Fetal Intestine Large	intestine
8	chr15:99836400-99852400	Weak transcription	Fetal Thymus	thymus
9	chr15:99836800-99852200	Weak transcription	Dnd41	blood
10	chr15:99837200-99851200	Weak transcription	Primary T cells from cord blood	blood
11	chr15:99847200-99856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:99847400-99851000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:99847400-99852400	Weak transcription	Liver	Liver
14	chr15:99847400-99852600	Weak transcription	Right Ventricle	heart
15	chr15:99847400-99854000	Weak transcription	Pancreas	Pancrea
16	chr15:99847400-99877200	Weak transcription	Ovary	ovary
17	chr15:99847600-99851200	Weak transcription	Psoas Muscle	Psoas
18	chr15:99847600-99852600	Weak transcription	Left Ventricle	heart
19	chr15:99847800-99852200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:99848000-99852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:99848200-99852400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:99848200-99852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:99848200-99860800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:99848400-99852000	Weak transcription	Brain Substantia Nigra	brain
25	chr15:99848400-99852200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:99848400-99852400	Weak transcription	Fetal Lung	lung
27	chr15:99848400-99852600	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:99848400-99860600	Weak transcription	HepG2	liver
29	chr15:99848400-99860800	Weak transcription	NH-A	brain
30	chr15:99849200-99852600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:99850400-99851200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:99850400-99863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:99850600-99851400	Enhancers	K562	blood
34	chr15:99850600-99851600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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