Variant report

Variant	rs2414104
Chromosome Location	chr15:51816671-51816672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51806249..51808093-chr15:51816177..51818172,2	MCF-7	breast:
2	chr15:51812082..51813725-chr15:51814759..51816922,2	K562	blood:
3	chr15:51813148..51814978-chr15:51814982..51816797,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11070850	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070852	0.91[ASN][1000 genomes]
rs11855041	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592390	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592422	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908028	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17704742	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869930	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2258064	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414108	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607111	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2607113	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28362471	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34604744	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359386	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4436729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4462536	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775945	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775950	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775967	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493498	0.88[ASN][1000 genomes]
rs6493502	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493504	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164999	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7176988	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8024233	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8025536	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030113	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030534	0.88[ASN][1000 genomes]
rs8034340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs930919	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][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	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv569405	chr15:51791559-51890282	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2414104	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51763600-51826800	Weak transcription	Colonic Mucosa	Colon
2	chr15:51776800-51837600	Weak transcription	Fetal Thymus	thymus
3	chr15:51776800-51855200	Weak transcription	Thymus	Thymus
4	chr15:51777600-51819000	Weak transcription	Small Intestine	intestine
5	chr15:51778400-51825800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:51780400-51817600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:51780400-51855800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:51780800-51839000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:51781400-51863000	Weak transcription	HSMM	muscle
10	chr15:51781600-51817400	Weak transcription	Brain Angular Gyrus	brain
11	chr15:51781600-51837000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:51785000-51827400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:51787200-51818400	Weak transcription	Primary T cells from cord blood	blood
14	chr15:51787400-51855400	Weak transcription	Osteobl	bone
15	chr15:51791800-51816800	Weak transcription	Lung	lung
16	chr15:51791800-51816800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:51792000-51817200	Weak transcription	Ovary	ovary
18	chr15:51792000-51817600	Weak transcription	Fetal Brain Male	brain
19	chr15:51792000-51819000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:51792200-51816800	Weak transcription	Fetal Intestine Large	intestine
21	chr15:51792200-51817000	Weak transcription	Brain Anterior Caudate	brain
22	chr15:51792200-51817000	Weak transcription	Fetal Lung	lung
23	chr15:51792200-51817000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:51792200-51817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:51792200-51817400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:51792200-51817400	Weak transcription	A549	lung
27	chr15:51792200-51817800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:51792200-51824000	Weak transcription	Fetal Kidney	kidney
29	chr15:51792200-51824000	Weak transcription	Left Ventricle	heart
30	chr15:51792400-51819000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:51792400-51819400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:51792400-51828600	Weak transcription	K562	blood
33	chr15:51792400-51838400	Weak transcription	HSMMtube	muscle
34	chr15:51792600-51817600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:51793000-51824000	Weak transcription	Dnd41	blood
36	chr15:51793800-51816800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:51794600-51861000	Weak transcription	Gastric	stomach
38	chr15:51795200-51816800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:51795200-51819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:51797600-51817400	Weak transcription	Hela-S3	cervix
41	chr15:51797800-51818000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:51798000-51817800	Weak transcription	Placenta	Placenta
43	chr15:51799000-51817000	Weak transcription	Fetal Intestine Small	intestine
44	chr15:51802400-51820600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr15:51804000-51823200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:51804400-51821200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:51805200-51816800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:51805400-51824000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:51807400-51823600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:51809000-51854800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links