Variant report

Variant	rs11621121
Chromosome Location	chr14:65822493-65822494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:65723600..65725474-chr14:65822150..65825144,2	MCF-7	breast:
2	chr14:65751559..65753214-chr14:65820526..65823180,2	MCF-7	breast:
3	chr14:65821204..65823382-chr14:65830299..65832860,2	MCF-7	breast:
4	chr14:65692463..65695041-chr14:65818683..65822827,3	MCF-7	breast:
5	chr14:65725388..65728499-chr14:65821707..65823714,3	MCF-7	breast:
6	chr14:65567238..65569298-chr14:65821601..65824153,2	MCF-7	breast:
7	chr14:65820651..65828097-chr14:65876794..65881062,12	MCF-7	breast:
8	chr14:65820274..65829265-chr14:65876318..65881127,26	MCF-7	breast:
9	chr14:65695112..65697010-chr14:65821133..65822947,2	MCF-7	breast:
10	chr14:65720634..65723404-chr14:65821648..65825451,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000125952	Chromatin interaction
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11158591	0.87[EUR][1000 genomes]
rs11621604	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11623920	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627402	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1256540	0.91[MEX][hapmap]
rs12878872	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12881755	0.88[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs12881911	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882269	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12886005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12886168	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12895337	0.96[ASN][1000 genomes]
rs1815654	0.88[EUR][1000 genomes]
rs1954052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899174	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902391	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143666	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7152441	0.90[ASN][1000 genomes]
rs7157006	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158347	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747541	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014475	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022094	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11621121	HIF1A	cis	cerebellum	SCAN
rs11621121	FUT8	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65812000-65822800	Weak transcription	Gastric	stomach
2	chr14:65813800-65823600	Weak transcription	Thymus	Thymus
3	chr14:65814000-65823400	Weak transcription	Small Intestine	intestine
4	chr14:65814000-65824800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr14:65814800-65823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:65815400-65824000	Weak transcription	Brain Angular Gyrus	brain
7	chr14:65816000-65822800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:65816800-65828000	Enhancers	Primary B cells from peripheral blood	blood
9	chr14:65818000-65823400	Enhancers	GM12878-XiMat	blood
10	chr14:65819600-65823200	Enhancers	Hela-S3	cervix
11	chr14:65819600-65823400	Enhancers	HMEC	breast
12	chr14:65819600-65823400	Enhancers	NHEK	skin
13	chr14:65819600-65823600	Enhancers	Stomach Mucosa	stomach
14	chr14:65819600-65824400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:65819600-65824800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:65819800-65824400	Enhancers	Placenta	Placenta
17	chr14:65819800-65824600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:65819800-65824800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr14:65820000-65823600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr14:65820200-65823000	Weak transcription	HUVEC	blood vessel
21	chr14:65820200-65823200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr14:65820200-65823200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:65820400-65822800	Weak transcription	HSMM	muscle
24	chr14:65820400-65823000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr14:65820400-65823000	Weak transcription	Osteobl	bone
26	chr14:65820400-65823200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr14:65820400-65823400	Weak transcription	A549	lung
28	chr14:65820600-65822600	Enhancers	Fetal Intestine Large	intestine
29	chr14:65821000-65822800	Enhancers	Fetal Intestine Small	intestine
30	chr14:65821200-65822800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr14:65821200-65823400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr14:65821200-65823600	Weak transcription	Primary B cells from cord blood	blood
33	chr14:65821400-65823200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:65821600-65822600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr14:65821600-65831600	Weak transcription	Esophagus	oesophagus
36	chr14:65821800-65822800	Weak transcription	NH-A	brain
37	chr14:65821800-65824000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr14:65821800-65824000	Weak transcription	Brain Hippocampus Middle	brain
39	chr14:65821800-65824000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr14:65821800-65824000	Weak transcription	Brain Substantia Nigra	brain
41	chr14:65821800-65824200	Weak transcription	Lung	lung
42	chr14:65821800-65828800	Weak transcription	Psoas Muscle	Psoas
43	chr14:65822000-65823400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:65822000-65823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr14:65822000-65823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr14:65822000-65824200	Weak transcription	Brain Anterior Caudate	brain
47	chr14:65822200-65823000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr14:65822200-65823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr14:65822200-65823400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr14:65822200-65824000	Enhancers	Primary T helper cells PMA-I stimulated	--

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