Variant report

Variant	rs1869084
Chromosome Location	chr11:3909286-3909287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10160254	0.81[ASN][1000 genomes]
rs10160331	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10160415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10160703	0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.81[ASN][1000 genomes]
rs10160753	0.81[ASN][1000 genomes]
rs10767679	0.90[CHD][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10767680	0.87[CHD][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10767681	0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10767684	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10767685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10835217	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10835226	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835231	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835232	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs10835236	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835238	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835239	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835247	0.81[ASN][1000 genomes]
rs10835248	0.81[ASN][1000 genomes]
rs10835249	0.86[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10835250	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10835252	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835256	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10835261	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10835262	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10835270	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs11030122	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11030176	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11030209	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs11030211	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1869085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4414209	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4622250	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4910584	0.90[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7111609	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7113148	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs7118295	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7120336	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7131437	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7131469	0.81[ASN][1000 genomes]
rs7932404	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
9	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	esv275356	chr11:3908738-3913014	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1869084	STIM1	cis	Thyroid	GTEx
rs1869084	OR51G2	cis	parietal	SCAN
rs1869084	IFITM3	cis	parietal	SCAN
rs1869084	TRIM21	cis	cerebellum	SCAN
rs1869084	CD81	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3888600-3911200	Weak transcription	Dnd41	blood
2	chr11:3889200-3913400	Weak transcription	Aorta	Aorta
3	chr11:3891400-3915000	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:3899200-3926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:3899800-3915600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:3900000-3916000	Weak transcription	Spleen	Spleen
7	chr11:3901200-3914600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:3902000-3911400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:3902200-3909400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:3902200-3914600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:3902200-3916400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:3902200-3916400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:3902400-3910400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr11:3902400-3916400	Weak transcription	Fetal Intestine Small	intestine
15	chr11:3902400-3923800	Weak transcription	Gastric	stomach
16	chr11:3905800-3911000	Weak transcription	K562	blood
17	chr11:3905800-3915200	Weak transcription	Esophagus	oesophagus
18	chr11:3905800-3915200	Weak transcription	Right Ventricle	heart
19	chr11:3906000-3913000	Weak transcription	Small Intestine	intestine
20	chr11:3906000-3914200	Weak transcription	Primary T cells from cord blood	blood
21	chr11:3906000-3914600	Enhancers	Primary B cells from cord blood	blood
22	chr11:3906000-3915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:3906000-3915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:3907000-3909600	Enhancers	HepG2	liver
25	chr11:3907000-3910000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:3907000-3910800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr11:3907000-3913200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:3907200-3910200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:3907200-3910200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:3907200-3912200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr11:3907200-3915600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:3907400-3914600	Weak transcription	Osteobl	bone
33	chr11:3907400-3915400	Weak transcription	Lung	lung
34	chr11:3907400-3915600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:3907400-3923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:3907600-3915400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:3907600-3922600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:3907800-3915200	Weak transcription	HMEC	breast
39	chr11:3908000-3910000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:3908000-3910000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr11:3908000-3910400	Enhancers	Psoas Muscle	Psoas
42	chr11:3908000-3912000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr11:3908200-3909600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr11:3908200-3909800	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:3908200-3909800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr11:3908200-3910200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr11:3908200-3910200	Enhancers	Fetal Muscle Leg	muscle
48	chr11:3908200-3910400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr11:3908200-3910400	Enhancers	GM12878-XiMat	blood
50	chr11:3908200-3914000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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