Variant report

Variant	rs6492958
Chromosome Location	chr15:40936606-40936607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10400825	0.85[EUR][1000 genomes]
rs10467972	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10744948	0.82[EUR][1000 genomes]
rs11070284	0.92[EUR][1000 genomes]
rs11070292	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs1142468	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11629680	0.83[EUR][1000 genomes]
rs11633367	0.87[EUR][1000 genomes]
rs11637239	0.83[EUR][1000 genomes]
rs11638204	0.82[EUR][1000 genomes]
rs11854763	0.92[EUR][1000 genomes]
rs12438182	0.81[EUR][1000 genomes]
rs12438955	0.92[EUR][1000 genomes]
rs12440468	0.85[EUR][1000 genomes]
rs12592882	0.88[EUR][1000 genomes]
rs12708401	0.92[EUR][1000 genomes]
rs12899600	0.86[EUR][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12912339	0.92[EUR][1000 genomes]
rs12915109	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916082	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17747351	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1901775	0.88[EUR][1000 genomes]
rs2278888	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2304580	1.00[CEU][hapmap]
rs2412541	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2619681	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3092978	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs34285050	0.83[EUR][1000 genomes]
rs4306472	0.85[EUR][1000 genomes]
rs4417527	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4420508	0.92[EUR][1000 genomes]
rs4439732	0.86[EUR][1000 genomes]
rs4924472	1.00[YRI][hapmap]
rs4924478	1.00[YRI][hapmap]
rs4924484	0.93[EUR][1000 genomes]
rs4924487	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4924490	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924491	0.88[EUR][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs55640412	0.85[EUR][1000 genomes]
rs6492957	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66885559	0.87[EUR][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161968	0.85[EUR][1000 genomes]
rs7162319	0.84[EUR][1000 genomes]
rs7162509	0.87[EUR][1000 genomes]
rs7164289	0.86[EUR][1000 genomes]
rs7167417	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7167768	0.80[EUR][1000 genomes]
rs7168873	0.88[EUR][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7171945	0.85[EUR][1000 genomes]
rs7172947	0.85[EUR][1000 genomes]
rs7176974	0.92[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7178486	0.92[EUR][1000 genomes]
rs72733486	0.80[EUR][1000 genomes]
rs8028999	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8031057	0.90[EUR][1000 genomes]
rs8035775	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs8037417	0.84[EUR][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs8038416	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs8041443	0.84[EUR][1000 genomes]
rs8042729	0.86[CEU][hapmap]
rs896796	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs936580	0.89[EUR][1000 genomes]
rs9806221	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6492958	RMDN3	cis	Muscle Skeletal	GTEx
rs6492958	RMDN3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
3	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:40900000-40943600	Weak transcription	NH-A	brain
9	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
10	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
13	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
14	chr15:40912600-40941400	Weak transcription	HepG2	liver
15	chr15:40913800-40986000	Weak transcription	A549	lung
16	chr15:40914400-40960000	Weak transcription	NHLF	lung
17	chr15:40914800-40942600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:40915600-40937000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:40915600-40937000	Weak transcription	HUVEC	blood vessel
20	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
22	chr15:40919800-40938400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr15:40922400-40938400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:40922600-40943800	Weak transcription	Hela-S3	cervix
26	chr15:40922800-40944000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:40922800-40944000	Weak transcription	NHEK	skin
28	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:40923200-40947000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
33	chr15:40924400-40943600	Weak transcription	Osteobl	bone
34	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
36	chr15:40926000-40947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:40927200-40942000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:40928200-40949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:40928200-40951200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:40928600-40945600	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:40931400-40944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:40932200-40941800	Weak transcription	Fetal Intestine Small	intestine
45	chr15:40932600-40946800	Weak transcription	Fetal Stomach	stomach
46	chr15:40933000-40938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:40933400-40937800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:40933800-40937600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:40933800-40941800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:40934000-40942400	Weak transcription	NHDF-Ad	bronchial

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