Variant report

Variant	rs10835232
Chromosome Location	chr11:3900133-3900134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3899401..3901421-chr11:3909382..3911737,2	K562	blood:
2	chr11:3898534..3901352-chr11:3914445..3916336,2	K562	blood:
3	chr11:3892574..3897220-chr11:3897647..3902052,8	K562	blood:
4	chr11:3875794..3876774-chr11:3900109..3901106,2	K562	blood:

Variant related genes	Relation type
ENSG00000229368	Chromatin interaction
ENSG00000228661	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10160254	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160331	0.99[ASN][1000 genomes]
rs10160415	0.99[ASN][1000 genomes]
rs10160703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160753	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767684	0.99[ASN][1000 genomes]
rs10767685	0.93[ASN][1000 genomes]
rs10835217	0.88[ASN][1000 genomes]
rs10835226	0.99[ASN][1000 genomes]
rs10835231	0.99[ASN][1000 genomes]
rs10835236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835238	0.99[ASN][1000 genomes]
rs10835239	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835245	0.99[ASN][1000 genomes]
rs10835246	0.99[ASN][1000 genomes]
rs10835247	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835248	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835250	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835252	0.99[ASN][1000 genomes]
rs10835256	0.98[ASN][1000 genomes]
rs10835261	0.96[ASN][1000 genomes]
rs10835262	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030122	0.89[ASN][1000 genomes]
rs11030176	0.99[ASN][1000 genomes]
rs11030209	1.00[JPT][hapmap]
rs11030211	0.85[JPT][hapmap]
rs12275981	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869084	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs1869085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs1964492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4414209	0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4598668	0.85[JPT][hapmap]
rs4622250	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4910582	0.85[GIH][hapmap]
rs4910584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7113148	1.00[JPT][hapmap]
rs7118295	0.98[ASN][1000 genomes]
rs7120336	0.99[ASN][1000 genomes]
rs7126870	0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs7131437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7131469	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10835232	OR56A5	cis	cerebellum	SCAN
rs10835232	FAM160A2	cis	cerebellum	SCAN
rs10835232	OR56A1	cis	parietal	SCAN
rs10835232	TRIM22	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3887200-3901400	Weak transcription	Brain Angular Gyrus	brain
2	chr11:3888600-3911200	Weak transcription	Dnd41	blood
3	chr11:3889000-3902400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr11:3889200-3913400	Weak transcription	Aorta	Aorta
5	chr11:3889400-3901200	Weak transcription	Lung	lung
6	chr11:3889400-3901400	Weak transcription	Fetal Stomach	stomach
7	chr11:3889800-3901200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:3891400-3915000	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:3892600-3901400	Weak transcription	Left Ventricle	heart
10	chr11:3894200-3902400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr11:3894800-3902200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr11:3894800-3902400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr11:3895000-3901800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:3895000-3902200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:3895200-3900800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:3895200-3902000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:3895200-3902400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr11:3895800-3902200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:3896000-3901200	Weak transcription	Right Ventricle	heart
20	chr11:3897000-3902400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:3897000-3903400	Enhancers	Primary B cells from cord blood	blood
22	chr11:3897200-3902200	Enhancers	Colon Smooth Muscle	Colon
23	chr11:3897200-3902200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr11:3897200-3903200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr11:3897400-3900600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:3897400-3900600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:3897400-3902800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr11:3897600-3900200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr11:3897600-3900600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:3897600-3902200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:3897600-3902600	Enhancers	Liver	Liver
32	chr11:3897800-3900200	Enhancers	Psoas Muscle	Psoas
33	chr11:3898000-3902400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr11:3898000-3902600	Flanking Active TSS	GM12878-XiMat	blood
35	chr11:3898000-3902800	Enhancers	Primary hematopoietic stem cells	blood
36	chr11:3898200-3902200	Enhancers	Stomach Mucosa	stomach
37	chr11:3898400-3902200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr11:3898400-3902200	Enhancers	Fetal Muscle Leg	muscle
39	chr11:3898400-3902400	Enhancers	Duodenum Mucosa	Duodenum
40	chr11:3898400-3902800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:3898600-3900200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:3898600-3900400	Enhancers	Pancreas	Pancrea
43	chr11:3898600-3900800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:3898600-3901000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr11:3898600-3902200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr11:3898600-3902400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr11:3898800-3900200	Enhancers	Gastric	stomach
48	chr11:3898800-3900400	Enhancers	Placenta	Placenta
49	chr11:3898800-3902200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:3898800-3903800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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