Variant report

Variant	rs12911229
Chromosome Location	chr15:75923054-75923055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10163126	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851882	0.81[EUR][1000 genomes]
rs11072552	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072553	0.85[ASN][1000 genomes]
rs11634402	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101874	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12909709	0.82[EUR][1000 genomes]
rs12910672	0.92[ASN][1000 genomes]
rs12916256	0.82[EUR][1000 genomes]
rs13737	0.84[ASN][1000 genomes]
rs28376842	0.83[EUR][1000 genomes]
rs4319732	0.83[EUR][1000 genomes]
rs4371118	0.92[ASN][1000 genomes]
rs4430707	0.83[EUR][1000 genomes]
rs4886449	0.83[EUR][1000 genomes]
rs4886450	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886452	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886718	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886719	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886720	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886722	0.92[ASN][1000 genomes]
rs7166281	0.87[ASN][1000 genomes]
rs7170787	0.88[ASN][1000 genomes]
rs7175223	0.90[ASN][1000 genomes]
rs7176989	0.81[EUR][1000 genomes]
rs8023495	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026113	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037089	0.92[ASN][1000 genomes]
rs8042772	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043300	0.82[EUR][1000 genomes]
rs9920028	0.91[ASN][1000 genomes]
rs9944207	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' 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	124 gene(s)	inside rSNPs	diseases
7	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12911229	MAN2C1	cis	Nerve Tibial	GTEx
rs12911229	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75918600-75931000	Weak transcription	Aorta	Aorta
2	chr15:75918800-75926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:75918800-75929200	Weak transcription	Brain Germinal Matrix	brain
4	chr15:75918800-75929400	Weak transcription	Psoas Muscle	Psoas
5	chr15:75918800-75929600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:75918800-75929600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:75918800-75929600	Weak transcription	Brain Anterior Caudate	brain
8	chr15:75918800-75929600	Weak transcription	Spleen	Spleen
9	chr15:75918800-75929600	Weak transcription	HSMM	muscle
10	chr15:75918800-75929800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:75918800-75930200	Weak transcription	HUVEC	blood vessel
12	chr15:75918800-75930400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75918800-75930600	Weak transcription	Right Atrium	heart
14	chr15:75919000-75929200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:75919000-75929400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:75919000-75929400	Weak transcription	Fetal Stomach	stomach
17	chr15:75919000-75929400	Weak transcription	Thymus	Thymus
18	chr15:75919000-75929600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:75919000-75929600	Weak transcription	Fetal Brain Female	brain
20	chr15:75919000-75929600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:75919000-75929800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:75919000-75929800	Weak transcription	Osteobl	bone
23	chr15:75919200-75926800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:75919200-75928000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:75919200-75928200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:75919200-75928200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:75919200-75928600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:75919200-75929400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:75919200-75929400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:75919200-75929600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:75919200-75929600	Weak transcription	Primary B cells from cord blood	blood
32	chr15:75919200-75929600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:75919200-75929600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:75919200-75929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:75919200-75929600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:75919200-75929600	Weak transcription	Fetal Lung	lung
37	chr15:75919200-75930200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:75919800-75929200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:75919800-75929600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr15:75920000-75926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:75920200-75929200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:75920200-75929400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:75920400-75924400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:75920400-75926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:75920400-75927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:75920400-75927600	Weak transcription	A549	lung
47	chr15:75920400-75928400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:75920600-75924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:75920600-75924400	Weak transcription	HMEC	breast
50	chr15:75920600-75930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links