Variant report

Variant	rs17793542
Chromosome Location	chr11:17946939-17946940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17944503..17947787-chr11:17948470..17951111,3	K562	blood:
2	chr11:17427284..17427815-chr11:17946414..17946944,2	MCF-7	breast:
3	chr11:17941038..17943989-chr11:17944479..17947250,2	MCF-7	breast:
4	chr11:17942744..17945115-chr11:17945670..17947778,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10741734	1.00[CEU][hapmap]
rs10766446	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024435	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024446	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11600873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11605018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12292490	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs12420936	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1401163	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1401164	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1401165	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1401166	1.00[CEU][hapmap]
rs1468291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1518521	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1607395	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs169806	0.96[CEU][hapmap]
rs1800532	0.96[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs188397	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1914710	0.89[YRI][hapmap]
rs2041244	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2056246	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2097816	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211095	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211096	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211098	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211107	0.96[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs211140	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211141	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]
rs211144	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211146	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211148	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211149	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211150	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211151	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2191091	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2237909	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237911	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237914	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237915	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237916	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237917	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237920	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283233	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283235	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2283237	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2299625	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2299628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2670764	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2670765	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs379388	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4141243	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4393297	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs508924	0.96[CEU][hapmap]
rs511604	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs517005	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs546383	0.96[CEU][hapmap];0.88[TSI][hapmap]
rs59573120	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs616099	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66813449	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684302	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs685657	0.87[CEU][hapmap]
rs72862028	0.81[EUR][1000 genomes]
rs728639	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs739916	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7927135	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7933505	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs887242	0.81[EUR][1000 genomes]
rs916975	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787863	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv5041	chr11:17946566-17947003	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2101877	chr11:17946590-17947033	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17793542	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs17793542	SERGEF	cis	Muscle Skeletal	GTEx
rs17793542	SAAL1	cis	parietal	SCAN
rs17793542	SAAL1	cis	cerebellum	SCAN
rs17793542	HTATIP2	cis	parietal	SCAN
rs17793542	SERGEF	cis	normal skin	skin_eQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17838400-17971600	Weak transcription	Gastric	stomach
2	chr11:17886000-17965200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:17896000-17968000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:17896400-17968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:17906000-17970200	Weak transcription	Lung	lung
6	chr11:17910600-17947000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:17914600-17965400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:17915800-17966000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:17917000-17947600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:17920600-17976000	Weak transcription	Esophagus	oesophagus
11	chr11:17928600-17970200	Weak transcription	Thymus	Thymus
12	chr11:17929200-17954800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:17933000-17956800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
15	chr11:17935200-17955000	Strong transcription	Primary T cells from cord blood	blood
16	chr11:17937400-17950600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:17937600-17949000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:17937600-17977000	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:17937800-17951800	Weak transcription	HSMMtube	muscle
20	chr11:17937800-17965800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:17939000-17950600	Weak transcription	Fetal Intestine Large	intestine
22	chr11:17939400-17953400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr11:17940000-17953000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:17940000-17976400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:17940600-17947800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:17941000-17953000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:17941400-17947800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:17942000-17950000	Enhancers	Liver	Liver
29	chr11:17942800-17954400	Weak transcription	NHEK	skin
30	chr11:17943200-17953400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr11:17943600-17950800	Weak transcription	Brain Anterior Caudate	brain
32	chr11:17943600-17952400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:17943600-17975400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:17943800-17950000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:17943800-17953200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:17943800-17992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:17944000-17948000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:17944000-17964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:17944000-17975600	Weak transcription	HSMM	muscle
40	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:17944200-17947000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:17944200-17948400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:17944200-17949000	Weak transcription	Fetal Intestine Small	intestine
44	chr11:17944200-17949800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:17944200-17950000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:17944200-17955400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:17944400-17947000	Enhancers	Psoas Muscle	Psoas
48	chr11:17944600-17948200	Weak transcription	Colonic Mucosa	Colon
49	chr11:17944800-17947800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr11:17945000-17948400	Weak transcription	NHDF-Ad	bronchial

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