Variant report

Variant	rs12534494
Chromosome Location	chr7:99629480-99629481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99626268..99629732-chr7:99646321..99649999,3	MCF-7	breast:
2	chr7:99626508..99630728-chr7:99630857..99634217,6	MCF-7	breast:
3	chr7:99629435..99632327-chr7:99685229..99688154,2	K562	blood:

Variant related genes	Relation type
ENSG00000166529	Chromatin interaction
ENSG00000168090	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1050542	0.80[ASN][1000 genomes]
rs1141057	0.94[ASN][1000 genomes]
rs12112428	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112642	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13309	0.82[ASN][1000 genomes]
rs1534309	0.84[ASN][1000 genomes]
rs2272338	0.85[ASN][1000 genomes]
rs2285886	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293481	0.89[ASN][1000 genomes]
rs34161112	0.89[ASN][1000 genomes]
rs35058708	0.94[ASN][1000 genomes]
rs35414630	0.94[ASN][1000 genomes]
rs4134917	0.85[ASN][1000 genomes]
rs4134923	0.85[ASN][1000 genomes]
rs4729567	0.96[ASN][1000 genomes]
rs4729568	0.96[ASN][1000 genomes]
rs4729571	0.90[ASN][1000 genomes]
rs4729572	0.85[ASN][1000 genomes]
rs4729577	0.90[ASN][1000 genomes]
rs62485010	0.84[ASN][1000 genomes]
rs6960432	0.90[ASN][1000 genomes]
rs941290	0.84[ASN][1000 genomes]
rs999886	0.86[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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	esv32694	chr7:99565608-99629919	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv1828033	chr7:99566252-99634770	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv1827496	chr7:99566264-99634782	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
8	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers 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 miRNA target site	1115 gene(s)	inside rSNPs	diseases
9	esv1824630	chr7:99614770-99639445	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12534494	AP4M1	cis	Adipose Subcutaneous	GTEx
rs12534494	ZKSCAN1	cis	multi-tissue	Pritchard
rs12534494	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs12534494	AP4M1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99614200-99639000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99615000-99632000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:99615200-99636400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:99615200-99637800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:99615400-99639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:99616400-99636200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:99618800-99630800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:99618800-99636400	Strong transcription	Dnd41	blood
9	chr7:99619000-99636000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr7:99619200-99636200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:99619200-99636200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:99619200-99636400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:99619200-99636400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:99619200-99636800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:99619400-99630800	Strong transcription	Fetal Stomach	stomach
16	chr7:99619400-99631000	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:99619400-99631800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr7:99619400-99632200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:99619400-99634000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:99619400-99635200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:99619400-99635200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:99619400-99635600	Strong transcription	Thymus	Thymus
23	chr7:99619400-99636200	Strong transcription	Fetal Brain Female	brain
24	chr7:99619400-99636400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:99619400-99637200	Strong transcription	Brain Germinal Matrix	brain
26	chr7:99619600-99631200	Strong transcription	Adipose Nuclei	Adipose
27	chr7:99619600-99631400	Strong transcription	HSMMtube	muscle
28	chr7:99619600-99636200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr7:99619800-99632000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:99619800-99634400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:99619800-99636200	Strong transcription	Brain Hippocampus Middle	brain
32	chr7:99620000-99636200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:99620000-99636400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr7:99620000-99636400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:99620200-99633800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:99620200-99635000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:99620400-99634200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:99620600-99629800	Strong transcription	Brain Substantia Nigra	brain
39	chr7:99620600-99632600	Strong transcription	Placenta	Placenta
40	chr7:99620600-99634400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr7:99620600-99636400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:99620800-99634000	Strong transcription	Left Ventricle	heart
43	chr7:99621000-99633000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr7:99621000-99633800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:99621200-99633400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:99621400-99633200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr7:99621400-99636600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:99621600-99633600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr7:99622000-99633000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr7:99622200-99630800	Strong transcription	Fetal Intestine Small	intestine

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