Variant report

Variant	rs7129830
Chromosome Location	chr11:34930239-34930240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34928494..34930891-chr11:34936071..34939196,3	MCF-7	breast:
2	chr11:34919773..34921558-chr11:34929230..34931688,2	K562	blood:
3	chr11:34928718..34934554-chr11:34935181..34939232,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149089	Chromatin interaction
ENSG00000110435	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10488801	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10488803	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10488804	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10488806	0.84[JPT][hapmap]
rs1049306	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1049307	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032922	0.80[ASN][1000 genomes]
rs11032923	0.80[ASN][1000 genomes]
rs11032927	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11032937	1.00[JPT][hapmap]
rs11032938	1.00[JPT][hapmap]
rs11032940	1.00[JPT][hapmap]
rs11032941	1.00[JPT][hapmap]
rs11032942	1.00[JPT][hapmap]
rs11032943	1.00[JPT][hapmap]
rs11500295	0.83[ASN][1000 genomes]
rs11500296	0.83[ASN][1000 genomes]
rs11500297	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11500298	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11500299	0.83[ASN][1000 genomes]
rs12271341	0.83[ASN][1000 genomes]
rs12273153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12273271	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12275620	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12275911	1.00[JPT][hapmap]
rs12276735	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12278245	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12278785	0.83[ASN][1000 genomes]
rs12283472	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12283652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283763	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12285604	0.83[ASN][1000 genomes]
rs12285752	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12286538	1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12288594	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12292719	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12293733	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12294125	1.00[JPT][hapmap]
rs16926295	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033356	1.00[ASN][1000 genomes]
rs2033359	0.83[ASN][1000 genomes]
rs2102475	0.83[ASN][1000 genomes]
rs2163377	0.83[ASN][1000 genomes]
rs2901525	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763926	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3763929	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3763931	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3763933	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3763934	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3763937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794165	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3794170	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3794171	0.83[ASN][1000 genomes]
rs3794172	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818393	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3818401	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3887071	0.83[ASN][1000 genomes]
rs3962032	0.83[ASN][1000 genomes]
rs57257751	0.83[ASN][1000 genomes]
rs58519774	0.83[ASN][1000 genomes]
rs6484746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101458	0.83[ASN][1000 genomes]
rs7102259	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7104943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7104984	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7110223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7111607	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7113708	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7115409	0.83[ASN][1000 genomes]
rs7116411	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7118017	0.83[ASN][1000 genomes]
rs7119958	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7126410	0.83[ASN][1000 genomes]
rs7126659	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7127669	0.83[ASN][1000 genomes]
rs7127715	0.83[ASN][1000 genomes]
rs7127846	0.83[ASN][1000 genomes]
rs7929220	0.83[ASN][1000 genomes]
rs7931454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938962	1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7941930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7947650	1.00[JPT][hapmap]
rs7952208	1.00[JPT][hapmap]
rs9804643	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv8807	chr11:34912167-34930289	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
rs7129830	APIP	cis	Thyroid	GTEx
rs7129830	APIP	cis	Whole Blood	GTEx
rs7129830	APIP	cis	Muscle Skeletal	GTEx
rs7129830	APIP	cis	lung	GTEx
rs7129830	APIP	cis	Adipose Subcutaneous	GTEx
rs7129830	APIP	cis	Esophagus Mucosa	GTEx
rs7129830	APIP	cis	Artery Tibial	GTEx
rs7129830	APIP	cis	Esophagus Muscularis	GTEx
rs7129830	APIP	cis	Heart Left Ventricle	GTEx
rs7129830	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34917600-34931000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:34920000-34935800	Weak transcription	Fetal Heart	heart
3	chr11:34922400-34936600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:34922400-34936600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:34922600-34936200	Weak transcription	Right Ventricle	heart
6	chr11:34922600-34936600	Weak transcription	NHEK	skin
7	chr11:34922800-34936600	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:34923000-34930400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:34923000-34931000	Weak transcription	Gastric	stomach
10	chr11:34923000-34931000	Weak transcription	Lung	lung
11	chr11:34923000-34934600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:34923000-34934600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:34923000-34936000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr11:34923000-34936800	Weak transcription	Colonic Mucosa	Colon
15	chr11:34923200-34936600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:34923200-34936600	Weak transcription	NHLF	lung
17	chr11:34923400-34935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:34923400-34935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:34923600-34935200	Weak transcription	NHDF-Ad	bronchial
20	chr11:34923600-34936200	Weak transcription	Fetal Intestine Large	intestine
21	chr11:34923600-34937200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:34923800-34932200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:34924000-34931000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:34924200-34932400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:34924200-34936200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:34924600-34931000	Weak transcription	Placenta	Placenta
27	chr11:34924800-34931000	Weak transcription	Fetal Stomach	stomach
28	chr11:34925000-34936600	Weak transcription	Fetal Kidney	kidney
29	chr11:34925000-34937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:34925200-34930600	Weak transcription	Primary T cells from cord blood	blood
31	chr11:34925200-34934400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:34925200-34936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:34925200-34936600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:34925600-34930400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:34925600-34930600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:34925600-34934400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:34925600-34936600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:34925600-34937000	Weak transcription	Ovary	ovary
39	chr11:34925800-34931600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:34926200-34936600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:34926400-34931000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:34926400-34931400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr11:34926400-34935400	Weak transcription	Dnd41	blood
44	chr11:34926400-34935600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:34927000-34931000	Weak transcription	Fetal Brain Male	brain
46	chr11:34927200-34931200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:34927200-34931600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:34927400-34930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:34927400-34931600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr11:34928200-34930600	Weak transcription	Fetal Muscle Leg	muscle

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