Variant report

Variant	rs11622989
Chromosome Location	chr14:71217013-71217014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71216108..71217908-chr14:71219307..71221968,2	MCF-7	breast:
2	chr14:71209875..71213128-chr14:71214251..71217560,3	K562	blood:
3	chr14:71214804..71217337-chr14:71274832..71276743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10873240	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11158881	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs11622104	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs11623147	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11844844	0.83[ASN][1000 genomes]
rs12433469	0.84[AMR][1000 genomes]
rs12437113	0.81[CHB][hapmap]
rs12437256	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12880887	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs12883087	0.83[AMR][1000 genomes]
rs12883244	0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs12895576	0.80[AMR][1000 genomes]
rs1548585	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17108510	0.85[AMR][1000 genomes]
rs17108537	0.82[ASN][1000 genomes]
rs17108539	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs17108548	0.81[CHB][hapmap]
rs1859464	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2332457	0.83[ASW][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34307438	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35438375	0.83[AMR][1000 genomes]
rs3829955	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4902847	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4902848	0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6573979	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67164415	0.81[ASN][1000 genomes]
rs71425385	0.81[ASN][1000 genomes]
rs7144786	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs7147731	0.84[AMR][1000 genomes]
rs7151405	0.85[AMR][1000 genomes]
rs7153601	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs7154907	0.85[AMR][1000 genomes]
rs7160912	0.83[MEX][hapmap];0.84[AMR][1000 genomes]
rs7161415	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72721934	0.82[AMR][1000 genomes]
rs731571	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs8005459	0.82[CEU][hapmap];0.93[AMR][1000 genomes]
rs8014356	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019156	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8022803	0.83[AMR][1000 genomes]
rs886600	0.89[ASW][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap]

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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11622989	DNAL1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
4	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
5	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
7	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
9	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
10	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr14:71199600-71219600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
16	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
17	chr14:71201600-71219000	Weak transcription	Lung	lung
18	chr14:71201600-71220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:71205000-71219000	Weak transcription	Brain Angular Gyrus	brain
21	chr14:71205400-71220400	Weak transcription	Small Intestine	intestine
22	chr14:71206000-71218200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr14:71206800-71221000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
25	chr14:71207000-71221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr14:71207000-71221800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr14:71209200-71229400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:71209400-71219000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr14:71209400-71219000	Weak transcription	Gastric	stomach
30	chr14:71209400-71219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:71209400-71221600	Weak transcription	Esophagus	oesophagus
32	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
33	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr14:71209600-71229000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr14:71210800-71217200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr14:71210800-71220600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:71211200-71217200	Strong transcription	HMEC	breast
39	chr14:71211600-71217200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
41	chr14:71212400-71218800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr14:71212600-71220200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr14:71213000-71217200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:71213000-71217200	Strong transcription	Primary B cells from cord blood	blood
45	chr14:71213800-71219000	Weak transcription	Pancreas	Pancrea
46	chr14:71214000-71220200	Strong transcription	NHEK	skin
47	chr14:71214400-71222000	Weak transcription	Psoas Muscle	Psoas
48	chr14:71215200-71217200	Strong transcription	Fetal Intestine Large	intestine
49	chr14:71215600-71221800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr14:71215600-71227000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links