Variant report

Variant	rs3781373
Chromosome Location	chr10:99080585-99080586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99051058..99054984-chr10:99078319..99082092,7	MCF-7	breast:
2	chr10:99050343..99055587-chr10:99077475..99082102,7	MCF-7	breast:
3	chr10:99051582..99055310-chr10:99077169..99083058,6	K562	blood:
4	chr10:99066690..99071389-chr10:99076606..99080814,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGAM1-4	chr10:99080498-99080991	NONHSAT015854

Variant related genes	Relation type
ENSG00000269891	Chromatin interaction
ENSG00000213390	Chromatin interaction
ENSG00000237169	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10736115	0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10736116	0.80[EUR][1000 genomes]
rs10748691	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs10748694	0.87[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs10786321	0.95[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10786323	0.85[EUR][1000 genomes]
rs10786324	0.81[EUR][1000 genomes]
rs10786326	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10786327	0.87[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10786329	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10786330	0.87[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10786332	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10786333	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10786334	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10786335	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882881	0.87[CEU][hapmap]
rs10882883	0.90[CEU][hapmap]
rs10882884	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs10882889	0.81[CEU][hapmap]
rs10882890	0.85[EUR][1000 genomes]
rs10882891	0.86[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10882894	0.83[EUR][1000 genomes]
rs10882897	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882898	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882899	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189120	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189122	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189127	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11189131	0.87[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs11189132	0.91[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11189137	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189138	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12221430	0.85[EUR][1000 genomes]
rs12413688	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12571098	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1334892	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468069	0.82[CEU][hapmap]
rs1572437	0.83[EUR][1000 genomes]
rs1890966	0.86[ASN][1000 genomes]
rs2297987	0.82[CEU][hapmap]
rs2861875	0.87[CEU][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs3740512	0.91[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740522	0.87[CEU][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs3814164	0.87[CEU][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs4917766	0.91[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4919087	0.87[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4919089	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4919090	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4919091	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61863767	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6584116	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7067835	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7076523	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7078288	0.91[CEU][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7080275	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7089634	0.87[EUR][1000 genomes]
rs7901853	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945187	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs945189	0.91[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
7	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv3375506	chr10:99078187-99080735	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3358377	chr10:99078587-99081135	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3781373	MORN4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99078000-99081200	Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr10:99078000-99081400	Active TSS	Monocytes-CD14+_RO01746	blood
3	chr10:99078200-99081000	Active TSS	Psoas Muscle	Psoas
4	chr10:99078200-99081200	Active TSS	Brain Angular Gyrus	brain
5	chr10:99078200-99081200	Active TSS	Colon Smooth Muscle	Colon
6	chr10:99078200-99081200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr10:99078200-99081600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr10:99078200-99081600	Active TSS	Rectal Smooth Muscle	rectum
9	chr10:99078400-99080600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:99078400-99080600	Active TSS	Small Intestine	intestine
11	chr10:99078400-99081000	Active TSS	Right Atrium	heart
12	chr10:99078400-99081200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr10:99078400-99081200	Active TSS	Stomach Mucosa	stomach
14	chr10:99078400-99081600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:99078600-99081200	Active TSS	Primary monocytes fromperipheralblood	blood
16	chr10:99079000-99082200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr10:99079400-99080600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr10:99079600-99080600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:99079600-99080600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:99079600-99080600	Flanking Active TSS	HMEC	breast
21	chr10:99079600-99080600	Flanking Active TSS	NHLF	lung
22	chr10:99079600-99081000	Bivalent/Poised TSS	Fetal Brain Female	brain
23	chr10:99079600-99081200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:99079600-99081400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:99079600-99081400	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr10:99079600-99081600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr10:99079600-99081600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:99079600-99081600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr10:99079600-99081600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr10:99079600-99081800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr10:99079600-99081800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:99079600-99082000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:99079800-99080600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:99079800-99080600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr10:99079800-99080600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
36	chr10:99079800-99080600	Flanking Active TSS	Hela-S3	cervix
37	chr10:99079800-99080800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
38	chr10:99079800-99081200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr10:99079800-99081400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:99079800-99081400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr10:99079800-99081400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr10:99079800-99081400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr10:99079800-99081400	Flanking Active TSS	Placenta	Placenta
44	chr10:99079800-99081400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr10:99079800-99081400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
46	chr10:99079800-99081400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr10:99079800-99081600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr10:99079800-99081600	Flanking Active TSS	Liver	Liver
49	chr10:99079800-99081800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
50	chr10:99079800-99082400	Flanking Active TSS	Primary B cells from cord blood	blood

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