Variant report

Variant	rs211141
Chromosome Location	chr11:17994314-17994315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17986603..17989181-chr11:17992411..17994723,3	MCF-7	breast:
2	chr11:17987462..17990448-chr11:17991474..17994357,2	K562	blood:
3	chr11:17754647..17756368-chr11:17993718..17995487,2	K562	blood:

Variant related genes	Relation type
ENSG00000129159	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10741734	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10766446	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832872	0.82[EUR][1000 genomes]
rs11024435	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024446	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11600873	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603299	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605018	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12292490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12420936	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1401163	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401164	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401165	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1401166	1.00[CEU][hapmap]
rs1468291	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1518521	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1518522	0.83[EUR][1000 genomes]
rs1607395	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs169806	0.96[CEU][hapmap]
rs172424	0.92[YRI][hapmap]
rs17793542	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1799913	0.80[EUR][1000 genomes]
rs1800532	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs188397	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041244	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056246	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2097816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211097	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211098	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211107	0.96[CEU][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap]
rs211114	0.85[YRI][hapmap]
rs211115	0.85[YRI][hapmap]
rs211119	0.80[YRI][hapmap]
rs211120	0.80[YRI][hapmap]
rs211121	0.80[YRI][hapmap]
rs211130	0.88[YRI][hapmap]
rs211131	0.92[YRI][hapmap]
rs211135	0.92[YRI][hapmap]
rs211137	0.91[YRI][hapmap]
rs211140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211144	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211149	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211150	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211151	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2191091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs2237907	0.80[EUR][1000 genomes]
rs2237908	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237911	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237913	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237914	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237916	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237917	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237920	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283237	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299625	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299628	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2670764	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs379388	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4141243	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393297	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs484616	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs508924	0.96[CEU][hapmap]
rs511604	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517005	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs546383	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs59573120	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs616099	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66813449	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs684302	0.92[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs685657	0.87[CEU][hapmap]
rs72862028	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs728639	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs739916	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7927135	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7933505	0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs887242	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs916975	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9787863	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs211141	SAAL1	cis	cerebellum	SCAN
rs211141	HTATIP2	cis	parietal	SCAN
rs211141	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs211141	SERGEF	cis	normal skin	skin_eQTL
rs211141	SAAL1	cis	parietal	SCAN
rs211141	SERGEF	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 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	chr11:17945400-18010000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:17959200-18007600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:17961000-18016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:17965400-17994400	Weak transcription	NH-A	brain
8	chr11:17966400-18014400	Weak transcription	Fetal Thymus	thymus
9	chr11:17968600-18007000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:17973800-18008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:17974200-18007000	Weak transcription	Fetal Lung	lung
13	chr11:17974400-18001200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:17974400-18007200	Weak transcription	Stomach Mucosa	stomach
15	chr11:17974400-18007400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:17974600-18008600	Weak transcription	K562	blood
17	chr11:17975000-18020200	Weak transcription	A549	lung
18	chr11:17976600-17994400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:17976600-17994400	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:17976600-17999000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:17976600-18006800	Weak transcription	Right Ventricle	heart
22	chr11:17976800-17994400	Weak transcription	Fetal Heart	heart
23	chr11:17977200-18000200	Weak transcription	Psoas Muscle	Psoas
24	chr11:17977400-18006800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:17977400-18007000	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:17977600-18008400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:17978200-17994400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:17978200-18016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:17978600-17998200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:17978600-18006800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:17979000-18005200	Weak transcription	Brain Anterior Caudate	brain
32	chr11:17979800-18016400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
34	chr11:17981000-17998800	Weak transcription	GM12878-XiMat	blood
35	chr11:17981200-17996200	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:17981200-18007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:17981200-18007800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:17981200-18008000	Weak transcription	Brain Substantia Nigra	brain
39	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
40	chr11:17981400-18005400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:17981600-17994400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:17981800-17995400	Weak transcription	Fetal Brain Male	brain
43	chr11:17982800-17998400	Weak transcription	Fetal Stomach	stomach
44	chr11:17982800-18005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:17983200-18006800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr11:17984200-18005600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr11:17986000-17995200	Strong transcription	HepG2	liver
48	chr11:17987200-18007000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr11:17988600-17997800	Strong transcription	Primary T cells from cord blood	blood
50	chr11:17989000-18006800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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