Variant report

Variant	rs935901
Chromosome Location	chr15:43651256-43651257
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	chr15:43645456..43647561-chr15:43650775..43652983,2	K562	blood:
2	chr15:43621538..43624484-chr15:43650651..43653663,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCMT2-1	chr15:43650376-43652236	NONHSAT042065

Variant related genes	Relation type
ENSG00000168803	Chromatin interaction
ENSG00000168806	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12324572	0.89[EUR][1000 genomes]
rs12440854	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16957627	0.89[EUR][1000 genomes]
rs16957630	0.89[EUR][1000 genomes]
rs16957632	0.89[EUR][1000 genomes]
rs1814538	0.87[CEU][hapmap]
rs2243434	0.88[CEU][hapmap]
rs2278860	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2412778	0.89[EUR][1000 genomes]
rs2412779	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2412780	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2439831	0.87[CEU][hapmap]
rs2444032	0.87[CEU][hapmap]
rs2467736	0.87[CEU][hapmap]
rs2467739	0.87[CEU][hapmap]
rs28415933	0.89[EUR][1000 genomes]
rs28461955	0.89[EUR][1000 genomes]
rs28578454	0.87[EUR][1000 genomes]
rs28594657	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28729853	0.87[EUR][1000 genomes]
rs28758627	0.97[EUR][1000 genomes]
rs2899082	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs3213990	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs3213991	0.87[EUR][1000 genomes]
rs3809481	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs4075674	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs4583210	0.89[EUR][1000 genomes]
rs527921	0.87[CEU][hapmap]
rs6493081	0.89[EUR][1000 genomes]
rs6493082	0.89[EUR][1000 genomes]
rs6493085	0.87[EUR][1000 genomes]
rs6493087	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6493088	0.87[EUR][1000 genomes]
rs689647	0.87[CEU][hapmap]
rs689781	0.87[CEU][hapmap]
rs690316	0.87[CEU][hapmap]
rs690436	0.87[CEU][hapmap]
rs694985	0.87[CEU][hapmap]
rs7163245	0.87[EUR][1000 genomes]
rs7165471	0.89[EUR][1000 genomes]
rs7170489	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs7173487	0.87[CEU][hapmap]
rs8039638	0.89[EUR][1000 genomes]
rs8041132	0.89[EUR][1000 genomes]
rs933941	0.86[EUR][1000 genomes]
rs956391	0.80[EUR][1000 genomes]
rs9652444	0.87[YRI][hapmap]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs935901	ELL3	cis	multi-tissue	Pritchard
rs935901	ADAL	cis	Adipose Subcutaneous	GTEx
rs935901	CATSPER2	cis	Esophagus Mucosa	GTEx
rs935901	ADAL	cis	lung	GTEx
rs935901	ADAL	cis	Nerve Tibial	GTEx
rs935901	ADAL	cis	multi-tissue	Pritchard
rs935901	SERF2	cis	multi-tissue	Pritchard
rs935901	ELL3	cis	Lymphoblastoid	GTEx
rs935901	ADAL	cis	Thyroid	GTEx
rs935901	ADAL	cis	Artery Aorta	GTEx
rs935901	CKMT1A	cis	Esophagus Mucosa	GTEx
rs935901	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs935901	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs935901	ADAL	cis	Artery Tibial	GTEx
rs935901	ADAL	cis	Esophagus Muscularis	GTEx
rs935901	ADAL	cis	Stomach	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
3	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:43641200-43652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:43641600-43652800	Weak transcription	Hela-S3	cervix
7	chr15:43643000-43651800	Weak transcription	Colonic Mucosa	Colon
8	chr15:43643400-43652800	Weak transcription	Right Ventricle	heart
9	chr15:43644400-43651800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr15:43646800-43656200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:43647200-43651400	Strong transcription	K562	blood
12	chr15:43647200-43652800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:43647200-43652800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:43648800-43652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:43648800-43653000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:43649200-43651400	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:43649200-43655400	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr15:43649200-43658600	ZNF genes & repeats	Liver	Liver
19	chr15:43649400-43652200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:43649600-43652800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:43649800-43651600	Strong transcription	Fetal Thymus	thymus
22	chr15:43649800-43653200	Strong transcription	Placenta	Placenta
23	chr15:43649800-43654000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr15:43649800-43660000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr15:43649800-43660200	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr15:43650000-43652800	Strong transcription	Brain Germinal Matrix	brain
27	chr15:43650200-43651400	Weak transcription	Fetal Stomach	stomach
28	chr15:43650200-43651600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:43650200-43652200	ZNF genes & repeats	Colon Smooth Muscle	Colon
30	chr15:43650200-43652800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:43650200-43652800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:43650200-43653000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:43650200-43655000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:43650200-43656800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
35	chr15:43650200-43657000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr15:43650200-43657400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:43650200-43657600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
38	chr15:43650200-43657800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:43650200-43657800	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr15:43650200-43658600	ZNF genes & repeats	GM12878-XiMat	blood
41	chr15:43650200-43659800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:43650200-43660400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr15:43650200-43661600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:43650400-43651600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:43650400-43652000	Strong transcription	Fetal Brain Male	brain
46	chr15:43650400-43652200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:43650400-43652400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:43650400-43652600	Strong transcription	Brain Anterior Caudate	brain
49	chr15:43650400-43652800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr15:43650400-43652800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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