Variant report

Variant	rs10494247
Chromosome Location	chr1:147113387-147113388
allele	A/G
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:147111969..147114581-chr1:147114883..147116475,2	MCF-7	breast:
2	chr1:147099364..147100021-chr1:147113282..147113974,2	MCF-7	breast:
3	chr1:146990186..146991720-chr1:147111335..147114236,2	MCF-7	breast:
4	chr1:146966391..146967425-chr1:147113261..147114425,11	MCF-7	breast:
5	chr1:147112261..147114414-chr1:147171374..147172710,13	MCF-7	breast:
6	chr1:147110556..147114398-chr1:147147907..147150571,4	MCF-7	breast:
7	chr1:147111761..147113944-chr1:147357488..147359944,2	MCF-7	breast:
8	chr1:147112511..147115637-chr1:147115937..147121176,5	MCF-7	breast:
9	chr1:146968843..146971407-chr1:147111788..147114623,2	MCF-7	breast:
10	chr1:146966519..146967415-chr1:147113356..147114363,3	MCF-7	breast:
11	chr1:147111228..147113732-chr1:147140739..147143080,2	MCF-7	breast:
12	chr1:146966419..146968529-chr1:147112636..147115549,2	MCF-7	breast:
13	chr1:147112272..147114709-chr1:147363667..147365778,2	MCF-7	breast:
14	chr1:147112679..147114292-chr1:147137123..147139321,2	MCF-7	breast:
15	chr1:147111649..147114275-chr1:147172459..147174573,2	MCF-7	breast:
16	chr1:147070799..147073693-chr1:147111124..147113890,4	MCF-7	breast:
17	chr1:146966147..146968131-chr1:147113029..147115620,2	MCF-7	breast:
18	chr1:147112207..147114432-chr1:147361910..147363394,12	MCF-7	breast:
19	chr1:146987573..146989081-chr1:147113048..147114594,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116128	Chromatin interaction
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10900387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12045115	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12132534	0.82[JPT][hapmap]
rs1344	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers 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 target site	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS 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 target site	29 gene(s)	inside rSNPs	diseases
19	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv482606	chr1:146959127-147134517	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
21	nsv872266	chr1:147020099-147381558	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
22	nsv831426	chr1:147089930-147265267	Strong transcription Weak transcription Enhancers Active TSS Flanking 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 target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10494247	ACP6	cis	Esophagus Muscularis	GTEx
rs10494247	ACP6	cis	Brain Pons	GTEx
rs10494247	ACP6	cis	Artery Tibial	GTEx
rs10494247	ACP6	cis	Thyroid	GTEx
rs10494247	ACP6	cis	multi-tissue	Pritchard
rs10494247	ACP6	Cis_1M	lymphoblastoid	RTeQTL
rs10494247	ACP6	cis	lymphoblastoid	seeQTL
rs10494247	ACP6	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147091800-147119800	Weak transcription	Hela-S3	cervix
2	chr1:147092200-147114000	Weak transcription	Fetal Kidney	kidney
3	chr1:147092800-147117600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:147096600-147113400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:147096600-147115000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:147096600-147115200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:147096600-147122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:147096800-147113400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:147096800-147114200	Weak transcription	Esophagus	oesophagus
10	chr1:147096800-147114200	Weak transcription	Ovary	ovary
11	chr1:147096800-147114400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:147096800-147115000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:147096800-147117000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:147096800-147117200	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:147096800-147119400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:147096800-147119400	Weak transcription	Aorta	Aorta
17	chr1:147096800-147119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:147096800-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:147096800-147119600	Weak transcription	Gastric	stomach
20	chr1:147096800-147119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:147096800-147119800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:147097000-147114400	Weak transcription	Fetal Brain Female	brain
23	chr1:147097000-147114400	Weak transcription	Thymus	Thymus
24	chr1:147097600-147130000	Weak transcription	Stomach Mucosa	stomach
25	chr1:147097800-147114600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:147097800-147115000	Weak transcription	Spleen	Spleen
27	chr1:147097800-147119800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:147097800-147124000	Weak transcription	Small Intestine	intestine
29	chr1:147098000-147119800	Weak transcription	Brain Germinal Matrix	brain
30	chr1:147098600-147117000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:147098800-147113600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:147099400-147119200	Weak transcription	Fetal Intestine Large	intestine
33	chr1:147100200-147114800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:147101600-147115000	Weak transcription	Primary T cells from cord blood	blood
35	chr1:147102200-147114400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:147102400-147117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:147102800-147120800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:147104200-147115000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:147104600-147114400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:147104800-147113600	Weak transcription	Fetal Stomach	stomach
41	chr1:147104800-147114200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:147104800-147119200	Weak transcription	Pancreas	Pancrea
43	chr1:147107400-147114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:147107400-147118200	Weak transcription	Primary B cells from cord blood	blood
45	chr1:147107800-147114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:147107800-147114400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:147108200-147114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:147109400-147124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:147111000-147113600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:147111000-147117600	Weak transcription	Brain Cingulate Gyrus	brain

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