Variant report

Variant	rs3829251
Chromosome Location	chr11:71194559-71194560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
2	chr11:71194336..71196595-chr11:71275951..71277679,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172890	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000254682	Chromatin interaction
ENSG00000204572	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10898186	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898191	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898193	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898201	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10898203	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898211	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898223	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898228	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898234	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898241	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11233933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11233977	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234027	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11234030	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11234042	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790349	0.80[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.90[ASN][1000 genomes]
rs7103591	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7114252	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7120029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7130829	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7940244	0.80[TSI][hapmap]
rs7949129	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1052432	chr11:71167449-71213007	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Vitamin D levels	20418485	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3829251	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs3829251	DHCR7	cis	parietal	SCAN
rs3829251	NADSYN1	cis	Nerve Tibial	GTEx
rs3829251	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs3829251	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3829251	KRTAP5-9	cis	parietal	SCAN
rs3829251	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs3829251	RP11-660L16.2	cis	Thyroid	GTEx
rs3829251	FOLR3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
3	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:71172200-71195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:71180600-71199000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:71180800-71197600	Strong transcription	Fetal Intestine Small	intestine
7	chr11:71180800-71198400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:71180800-71199400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr11:71182000-71197600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:71182000-71197800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:71182000-71198400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr11:71182000-71198800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:71182200-71195800	Strong transcription	Lung	lung
17	chr11:71182200-71197800	Strong transcription	Brain Cingulate Gyrus	brain
18	chr11:71182200-71197800	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr11:71182200-71198000	Strong transcription	Brain Hippocampus Middle	brain
20	chr11:71182200-71198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:71182200-71198400	Strong transcription	Brain Anterior Caudate	brain
22	chr11:71182200-71198600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:71182200-71198600	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:71182200-71198600	Strong transcription	Fetal Stomach	stomach
25	chr11:71182200-71211000	Strong transcription	Liver	Liver
26	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
30	chr11:71182400-71197000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr11:71182400-71197600	Strong transcription	Colonic Mucosa	Colon
32	chr11:71182400-71197800	Strong transcription	Primary B cells from cord blood	blood
33	chr11:71182400-71197800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:71182400-71197800	Strong transcription	Aorta	Aorta
35	chr11:71182400-71197800	Strong transcription	Brain Angular Gyrus	brain
36	chr11:71182400-71197800	Strong transcription	Fetal Brain Female	brain
37	chr11:71182400-71197800	Strong transcription	Fetal Intestine Large	intestine
38	chr11:71182400-71197800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr11:71182400-71198200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:71182400-71198200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:71182400-71198400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:71182400-71198400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr11:71182400-71198400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:71182400-71198800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:71182400-71198800	Strong transcription	GM12878-XiMat	blood
46	chr11:71182400-71199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:71182400-71199600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:71182400-71199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:71182400-71213800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links