Variant report

Variant	rs887242
Chromosome Location	chr11:18021316-18021317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18007709..18010705-chr11:18020081..18022716,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10741734	0.89[EUR][1000 genomes]
rs10766446	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832872	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10832874	0.85[EUR][1000 genomes]
rs11024446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600873	0.81[EUR][1000 genomes]
rs11605018	0.81[EUR][1000 genomes]
rs12292490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401163	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401164	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401165	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1518521	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1518522	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1607395	0.88[EUR][1000 genomes]
rs169806	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17793542	0.81[EUR][1000 genomes]
rs1799913	0.88[EUR][1000 genomes]
rs1800532	0.88[EUR][1000 genomes]
rs188397	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2041244	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2056246	0.87[EUR][1000 genomes]
rs2071532	0.84[EUR][1000 genomes]
rs2097816	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs211095	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211096	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs211097	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs211098	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs211106	0.82[EUR][1000 genomes]
rs211107	0.86[EUR][1000 genomes]
rs211108	0.86[EUR][1000 genomes]
rs211140	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs211141	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs211144	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211146	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs211148	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211149	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211150	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211151	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237907	0.88[EUR][1000 genomes]
rs2237908	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237909	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237911	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237913	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237914	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237915	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237916	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237917	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2237920	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2283233	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283235	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283237	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299625	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299628	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2670764	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2670765	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs508924	0.86[EUR][1000 genomes]
rs511604	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs517005	0.82[EUR][1000 genomes]
rs544437	0.80[EUR][1000 genomes]
rs546383	0.83[EUR][1000 genomes]
rs572940	0.81[EUR][1000 genomes]
rs593839	0.85[EUR][1000 genomes]
rs616099	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652458	0.86[EUR][1000 genomes]
rs654734	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs66813449	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684302	0.86[EUR][1000 genomes]
rs685657	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72862028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728639	0.81[EUR][1000 genomes]
rs7927135	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7933505	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs916975	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9787863	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs887242	SERGEF	cis	Muscle Skeletal	GTEx
rs887242	SERGEF	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
2	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
6	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
7	chr11:17989400-18023400	Weak transcription	Gastric	stomach
8	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
9	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
12	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18008200-18025800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:18008400-18023800	Weak transcription	Fetal Lung	lung
18	chr11:18008400-18026800	Weak transcription	NH-A	brain
19	chr11:18008600-18022600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
21	chr11:18008800-18025800	Weak transcription	NHEK	skin
22	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
24	chr11:18009200-18021600	Weak transcription	Fetal Intestine Small	intestine
25	chr11:18009200-18026200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:18009200-18026800	Weak transcription	K562	blood
27	chr11:18009400-18033600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:18010200-18022800	Weak transcription	Thymus	Thymus
29	chr11:18010200-18033600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:18010400-18022800	Weak transcription	Right Ventricle	heart
31	chr11:18010400-18033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:18010600-18026000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:18013800-18029400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr11:18014200-18028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:18014200-18028600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:18014200-18029000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr11:18014200-18029200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr11:18014200-18029800	Strong transcription	Primary T cells from cord blood	blood
39	chr11:18014600-18028000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:18014600-18028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:18014800-18033200	Weak transcription	Stomach Mucosa	stomach
42	chr11:18015000-18022400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:18015200-18033400	Weak transcription	Fetal Heart	heart
44	chr11:18015400-18027400	Weak transcription	Hela-S3	cervix
45	chr11:18016000-18025000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:18016200-18026400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:18016200-18028800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr11:18016400-18033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:18016800-18023800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:18017000-18023400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links