Variant report

Variant	rs1105881
Chromosome Location	chr15:42072530-42072531
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	chr15:42061280..42063508-chr15:42070993..42072761,2	K562	blood:
2	chr15:42064976..42070217-chr15:42070811..42075517,5	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1107858	0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs11632424	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11635067	0.85[AMR][1000 genomes]
rs11635415	0.84[AMR][1000 genomes]
rs12440747	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs12441300	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1531140	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs16952372	0.92[JPT][hapmap]
rs17676742	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs17677199	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs17677991	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs17678138	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs17678552	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17678767	0.92[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17734856	0.96[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1918310	0.96[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241522	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs2277535	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2303516	0.89[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2303518	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs2305654	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs2412641	0.85[AMR][1000 genomes]
rs28373318	0.80[AMR][1000 genomes]
rs28401754	0.85[AMR][1000 genomes]
rs28432037	0.85[AMR][1000 genomes]
rs28451764	0.82[AMR][1000 genomes]
rs28680296	0.85[AMR][1000 genomes]
rs28701757	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28754734	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3179542	0.80[AMR][1000 genomes]
rs3743024	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs3959569	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4923905	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs4923914	0.88[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4923915	0.85[AMR][1000 genomes]
rs4924570	0.85[JPT][hapmap]
rs4924575	0.92[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924576	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs4924580	0.80[AMR][1000 genomes]
rs62002090	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62002091	0.84[AMR][1000 genomes]
rs8025714	0.84[AMR][1000 genomes]
rs890498	0.84[AMR][1000 genomes]
rs890505	0.85[AMR][1000 genomes]
rs9672298	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9672360	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs9920903	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Educational attainment	25201988	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1105881	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs1105881	MGA	cis	lesional skin	skin_eQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42067600-42083000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:42068000-42075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42068000-42078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:42068200-42073600	Enhancers	HepG2	liver
5	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42068400-42072800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr15:42068400-42073000	Enhancers	Brain Hippocampus Middle	brain
8	chr15:42068400-42073800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:42068400-42074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:42068400-42075200	Weak transcription	Pancreas	Pancrea
11	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:42068600-42072600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr15:42068600-42073000	Weak transcription	Placenta	Placenta
14	chr15:42068600-42073200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:42068600-42073800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:42068600-42073800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:42068800-42072800	Enhancers	Brain Anterior Caudate	brain
19	chr15:42068800-42073200	Enhancers	Colon Smooth Muscle	Colon
20	chr15:42068800-42074400	Weak transcription	Primary B cells from cord blood	blood
21	chr15:42068800-42074400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:42069200-42075200	Weak transcription	K562	blood
23	chr15:42069400-42075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:42069600-42073200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr15:42069800-42075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:42069800-42075200	Weak transcription	Gastric	stomach
27	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
29	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:42070200-42073200	Enhancers	NHLF	lung
31	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
32	chr15:42070600-42072800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr15:42070800-42072600	Enhancers	NH-A	brain
34	chr15:42070800-42075000	Weak transcription	Dnd41	blood
35	chr15:42071000-42073200	Enhancers	Brain Substantia Nigra	brain
36	chr15:42071000-42074800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:42071200-42072600	Weak transcription	Small Intestine	intestine
41	chr15:42071200-42074000	Enhancers	HUVEC	blood vessel
42	chr15:42071200-42074400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:42071200-42074600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
45	chr15:42071400-42072600	Genic enhancers	Fetal Intestine Small	intestine
46	chr15:42071600-42072600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:42071600-42072800	Enhancers	Left Ventricle	heart
48	chr15:42071600-42072800	Enhancers	Ovary	ovary
49	chr15:42071600-42073000	Genic enhancers	NHEK	skin
50	chr15:42071600-42073200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links