Variant report

Variant	rs10835239
Chromosome Location	chr11:3907379-3907380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:3907040-3907572	SK-N-SH	brain:	n/a	chr11:3907344-3907360
2	GATA2	chr11:3906981-3907740	HUVEC	blood vessel:	n/a	chr11:3907344-3907360 chr11:3907343-3907357
3	GATA3	chr11:3907054-3907578	SK-N-SH	brain:	n/a	chr11:3907344-3907360
4	FOS	chr11:3907145-3907480	MCF10A-Er-Src	breast:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
5	FOSL1	chr11:3906933-3907662	HCT-116	colon:	n/a	chr11:3907299-3907308 chr11:3907301-3907308
6	JUN	chr11:3907128-3907466	HUVEC	blood vessel:	n/a	chr11:3907299-3907308 chr11:3907301-3907308
7	FOS	chr11:3907110-3907511	HUVEC	blood vessel:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
8	MAX	chr11:3906941-3907467	HCT-116	colon:	n/a	n/a
9	FOS	chr11:3907162-3907474	MCF10A-Er-Src	breast:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
10	POLR2A	chr11:3907054-3907454	HUVEC	blood vessel:	n/a	n/a
11	JUND	chr11:3906944-3907607	HCT-116	colon:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
12	FOS	chr11:3907244-3907380	MCF10A-Er-Src	breast:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
13	FOS	chr11:3907151-3907380	MCF10A-Er-Src	breast:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
14	TCF7L2	chr11:3907076-3907460	HCT-116	colon:	n/a	chr11:3907300-3907309 chr11:3907299-3907308
15	ZNF263	chr11:3907049-3907397	HEK293-T-REx	kidney:	n/a	n/a
16	JUND	chr11:3907280-3907430	HepG2	liver:	n/a	chr11:3907299-3907308 chr11:3907301-3907308 chr11:3907298-3907309
17	SP1	chr11:3906900-3907598	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3906079..3908316-chr11:3988710..3990857,2	K562	blood:
2	chr11:3906664..3909533-chr11:3913263..3915649,2	K562	blood:
3	chr11:3906966..3908700-chr11:3915127..3916837,2	MCF-7	breast:
4	chr11:3900708..3902267-chr11:3904917..3907387,2	K562	blood:

Variant related genes	Relation type
STIM1	TF binding region
ENSG00000230593	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1013351	0.82[CEU][hapmap]
rs10160254	0.99[ASN][1000 genomes]
rs10160331	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160415	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160703	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10160753	0.99[ASN][1000 genomes]
rs10500590	0.81[CEU][hapmap]
rs10767679	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10767680	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10767681	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10767684	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767685	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10767702	0.86[CEU][hapmap]
rs10767715	0.81[CEU][hapmap]
rs10835217	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835226	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835231	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835232	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835245	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835246	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835247	0.99[ASN][1000 genomes]
rs10835248	0.99[ASN][1000 genomes]
rs10835249	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835250	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835252	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835256	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835261	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835311	0.82[CEU][hapmap]
rs10835331	0.81[CEU][hapmap]
rs10835340	0.81[CEU][hapmap]
rs10835399	0.81[CEU][hapmap]
rs10835402	0.86[CEU][hapmap]
rs10835403	0.81[CEU][hapmap]
rs10835406	0.82[CEU][hapmap]
rs10835407	0.81[CEU][hapmap]
rs11030122	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030176	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030209	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs11030211	0.85[JPT][hapmap]
rs11030276	0.82[CEU][hapmap]
rs11030660	0.82[CEU][hapmap]
rs12223176	0.82[CEU][hapmap]
rs12275981	0.91[ASN][1000 genomes]
rs12286710	0.81[CEU][hapmap]
rs1349583	0.81[CEU][hapmap]
rs1452047	0.81[CEU][hapmap]
rs17081	0.81[CEU][hapmap]
rs17279635	0.81[CEU][hapmap]
rs1869084	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1869085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964492	0.84[ASN][1000 genomes]
rs2898947	0.81[CEU][hapmap]
rs4414209	0.95[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4598668	0.80[JPT][hapmap]
rs4622250	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4910584	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4910868	0.86[CEU][hapmap]
rs7102215	0.82[CEU][hapmap]
rs7111609	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs7113148	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs7118295	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120336	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128762	0.82[CEU][hapmap]
rs7131437	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131469	0.99[ASN][1000 genomes]
rs7950153	0.81[CEU][hapmap]
rs995498	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10835239	STIM1	cis	Thyroid	GTEx

Chromatin state (count:69 , 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	chr11:3902200-3908200	Weak transcription	Adipose Nuclei	Adipose
10	chr11:3902200-3908400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:3902200-3909200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:3902200-3909200	Weak transcription	Fetal Thymus	thymus
13	chr11:3902200-3909200	Weak transcription	Thymus	Thymus
14	chr11:3902200-3909400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:3902200-3914600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:3902200-3916400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:3902200-3916400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:3902400-3909200	Weak transcription	Left Ventricle	heart
19	chr11:3902400-3910400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr11:3902400-3916400	Weak transcription	Fetal Intestine Small	intestine
21	chr11:3902400-3923800	Weak transcription	Gastric	stomach
22	chr11:3902800-3908200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:3903600-3907400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr11:3905400-3908200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:3905600-3907600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:3905600-3907800	Enhancers	HMEC	breast
27	chr11:3905600-3908200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:3905800-3911000	Weak transcription	K562	blood
29	chr11:3905800-3915200	Weak transcription	Esophagus	oesophagus
30	chr11:3905800-3915200	Weak transcription	Right Ventricle	heart
31	chr11:3906000-3908200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr11:3906000-3908400	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:3906000-3913000	Weak transcription	Small Intestine	intestine
34	chr11:3906000-3914200	Weak transcription	Primary T cells from cord blood	blood
35	chr11:3906000-3914600	Enhancers	Primary B cells from cord blood	blood
36	chr11:3906000-3915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:3906000-3915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:3906200-3907800	Enhancers	NHEK	skin
39	chr11:3906200-3908200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:3906200-3908200	Weak transcription	GM12878-XiMat	blood
41	chr11:3906800-3907400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr11:3906800-3907400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:3906800-3907600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:3906800-3907800	Enhancers	HUVEC	blood vessel
45	chr11:3907000-3907400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:3907000-3907400	Enhancers	Lung	lung
47	chr11:3907000-3907400	Enhancers	Ovary	ovary
48	chr11:3907000-3907400	Enhancers	Hela-S3	cervix
49	chr11:3907000-3907400	Enhancers	NH-A	brain
50	chr11:3907000-3907600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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