Variant report

Variant	rs11687498
Chromosome Location	chr2:48737596-48737597
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48731834..48734173-chr2:48736492..48738374,2	K562	blood:
2	chr2:48736001..48737694-chr2:48761849..48763956,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11675947	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11679685	0.80[AMR][1000 genomes]
rs11683444	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11687771	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11689285	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11689288	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11690526	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11693784	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2937	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34026270	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34242961	0.87[AFR][1000 genomes]
rs34542838	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4364065	0.80[AMR][1000 genomes]
rs7570877	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11687498	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
2	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
5	chr2:48722600-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
7	chr2:48724400-48738400	Weak transcription	Fetal Heart	heart
8	chr2:48726200-48742400	Weak transcription	Colonic Mucosa	Colon
9	chr2:48726400-48737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:48728200-48756800	Weak transcription	HMEC	breast
12	chr2:48728600-48738400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:48728800-48737600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:48728800-48741800	Weak transcription	Spleen	Spleen
15	chr2:48729000-48742800	Weak transcription	Right Ventricle	heart
16	chr2:48729600-48742800	Weak transcription	Esophagus	oesophagus
17	chr2:48729800-48738200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:48732400-48740000	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:48732400-48743400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
22	chr2:48732800-48740000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:48733400-48742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:48734200-48739800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:48735000-48737600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:48735000-48738000	Enhancers	NHDF-Ad	bronchial
27	chr2:48735200-48738000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:48735200-48738000	Enhancers	HUVEC	blood vessel
29	chr2:48735200-48738200	Enhancers	Hela-S3	cervix
30	chr2:48735200-48738400	Weak transcription	Lung	lung
31	chr2:48735200-48739600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:48735400-48737600	Genic enhancers	Primary T cells from cord blood	blood
33	chr2:48735400-48737800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:48735400-48737800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr2:48735400-48738000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:48735400-48738000	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:48735400-48738000	Enhancers	NH-A	brain
38	chr2:48735400-48740200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:48735400-48740400	Strong transcription	Brain Germinal Matrix	brain
40	chr2:48735600-48737800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:48735600-48738000	Enhancers	Fetal Kidney	kidney
42	chr2:48735600-48740200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:48735800-48737600	Enhancers	Fetal Intestine Small	intestine
44	chr2:48735800-48738400	Weak transcription	Fetal Stomach	stomach
45	chr2:48736000-48737600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:48736000-48737800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:48736000-48738200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:48736000-48738200	Enhancers	Osteobl	bone
49	chr2:48736000-48738400	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:48736000-48738400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links