Variant report

Variant	rs7104943
Chromosome Location	chr11:34935122-34935123
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	chr11:34932335..34935204-chr11:34935436..34938565,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149089	Chromatin interaction
ENSG00000110435	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10488801	0.83[ASN][1000 genomes]
rs1049306	0.83[ASN][1000 genomes]
rs1049307	0.83[ASN][1000 genomes]
rs11032922	0.80[ASN][1000 genomes]
rs11032923	0.80[ASN][1000 genomes]
rs11032925	0.83[ASN][1000 genomes]
rs11032926	0.83[ASN][1000 genomes]
rs11032927	0.83[ASN][1000 genomes]
rs11500298	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12273153	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12276735	0.83[ASN][1000 genomes]
rs12282552	0.83[ASN][1000 genomes]
rs12283472	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12283652	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12283763	0.83[ASN][1000 genomes]
rs12286538	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12293733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16926295	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16926431	0.83[ASN][1000 genomes]
rs16926448	0.83[ASN][1000 genomes]
rs2033356	0.96[ASN][1000 genomes]
rs2901525	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763924	0.83[ASN][1000 genomes]
rs3763925	0.83[ASN][1000 genomes]
rs3763926	0.83[ASN][1000 genomes]
rs3763929	0.83[ASN][1000 genomes]
rs3763930	0.83[ASN][1000 genomes]
rs3763931	0.83[ASN][1000 genomes]
rs3763932	0.83[ASN][1000 genomes]
rs3763933	0.83[ASN][1000 genomes]
rs3763934	0.83[ASN][1000 genomes]
rs3763935	0.83[ASN][1000 genomes]
rs3763936	0.83[ASN][1000 genomes]
rs3763937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794166	0.83[ASN][1000 genomes]
rs3794170	0.83[ASN][1000 genomes]
rs3794172	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818393	0.83[ASN][1000 genomes]
rs3818396	0.83[ASN][1000 genomes]
rs3818397	0.83[ASN][1000 genomes]
rs3818401	0.83[ASN][1000 genomes]
rs6484746	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7104418	0.83[ASN][1000 genomes]
rs7104829	0.83[ASN][1000 genomes]
rs7104984	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7105141	0.83[ASN][1000 genomes]
rs7105167	0.83[ASN][1000 genomes]
rs7105174	0.83[ASN][1000 genomes]
rs7116386	0.83[ASN][1000 genomes]
rs7116411	0.83[ASN][1000 genomes]
rs7121117	0.83[ASN][1000 genomes]
rs7121341	0.83[ASN][1000 genomes]
rs7126659	0.83[ASN][1000 genomes]
rs7129830	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7130867	0.80[ASN][1000 genomes]
rs7130874	0.80[ASN][1000 genomes]
rs7131118	0.83[ASN][1000 genomes]
rs7924409	0.80[ASN][1000 genomes]
rs7931454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938962	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7941930	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952624	0.80[ASN][1000 genomes]
rs7952629	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2757436	chr11:34913315-34963728	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759817	chr11:34913315-34963728	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
5	esv34511	chr11:34914124-34942836	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	esv2756165	chr11:34914137-34942836	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7104943	APIP	cis	lung	GTEx
rs7104943	APIP	cis	Adipose Subcutaneous	GTEx
rs7104943	APIP	cis	Whole Blood	GTEx
rs7104943	APIP	cis	Artery Tibial	GTEx
rs7104943	APIP	cis	Heart Left Ventricle	GTEx
rs7104943	APIP	cis	Esophagus Muscularis	GTEx
rs7104943	APIP	cis	Thyroid	GTEx
rs7104943	APIP	cis	Muscle Skeletal	GTEx
rs7104943	APIP	cis	Esophagus Mucosa	GTEx
rs7104943	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34920000-34935800	Weak transcription	Fetal Heart	heart
2	chr11:34922400-34936600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:34922400-34936600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:34922600-34936200	Weak transcription	Right Ventricle	heart
5	chr11:34922600-34936600	Weak transcription	NHEK	skin
6	chr11:34922800-34936600	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:34923000-34936000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr11:34923000-34936800	Weak transcription	Colonic Mucosa	Colon
9	chr11:34923200-34936600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:34923200-34936600	Weak transcription	NHLF	lung
11	chr11:34923400-34935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:34923600-34935200	Weak transcription	NHDF-Ad	bronchial
13	chr11:34923600-34936200	Weak transcription	Fetal Intestine Large	intestine
14	chr11:34923600-34937200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:34924200-34936200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:34925000-34936600	Weak transcription	Fetal Kidney	kidney
17	chr11:34925000-34937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:34925200-34936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:34925200-34936600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:34925600-34936600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:34925600-34937000	Weak transcription	Ovary	ovary
22	chr11:34926200-34936600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:34926400-34935400	Weak transcription	Dnd41	blood
24	chr11:34926400-34935600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:34929200-34937000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr11:34929400-34936600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:34929400-34936600	Weak transcription	Osteobl	bone
28	chr11:34929800-34936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:34930200-34936200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:34930200-34937000	Weak transcription	Aorta	Aorta
31	chr11:34930400-34936600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:34930600-34936600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:34930600-34936600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:34930800-34936600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:34931000-34935400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:34931200-34936000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:34931200-34936600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr11:34931200-34936600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:34931200-34937000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:34931200-34937000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr11:34931200-34937000	Weak transcription	Esophagus	oesophagus
42	chr11:34931200-34937000	Weak transcription	Lung	lung
43	chr11:34931400-34936600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:34931400-34936600	Weak transcription	A549	lung
45	chr11:34931400-34936600	Weak transcription	HSMM	muscle
46	chr11:34931400-34937000	Weak transcription	Placenta	Placenta
47	chr11:34931400-34937000	Weak transcription	Gastric	stomach
48	chr11:34931600-34935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:34931600-34936600	Weak transcription	Brain Substantia Nigra	brain
50	chr11:34931800-34935400	Weak transcription	Primary hematopoietic stem cells	blood

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