Variant report

Variant	rs10900376
Chromosome Location	chr1:147013362-147013363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:147011744..147014234-chr1:147070783..147073063,3	K562	blood:
2	chr1:147012761..147015831-chr1:147068894..147072363,4	MCF-7	breast:
3	chr1:147011744..147014234-chr1:147070783..147072314,2	K562	blood:
4	chr1:147008733..147014706-chr1:147069097..147075030,9	MCF-7	breast:
5	chr1:147010483..147014086-chr1:147140786..147143809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116128	Chromatin interaction
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1015235	0.85[JPT][hapmap]
rs10793689	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583944	0.90[JPT][hapmap]
rs12127408	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132440	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2353544	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3806218	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4950460	0.83[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666569	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6666306	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs6676804	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv831414	chr1:146884994-147083866	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	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
21	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10900376	PGAP1	trans	parietal	SCAN
rs10900376	ACP6	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147012000-147013400	Weak transcription	Small Intestine	intestine
2	chr1:147012000-147014000	Flanking Active TSS	Dnd41	blood
3	chr1:147012000-147014800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:147012000-147015000	Active TSS	Fetal Kidney	kidney
5	chr1:147012200-147013400	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:147012200-147014800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr1:147012400-147013400	Flanking Active TSS	HepG2	liver
8	chr1:147012400-147014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:147012400-147014800	Active TSS	Aorta	Aorta
10	chr1:147012400-147014800	Active TSS	Right Atrium	heart
11	chr1:147012400-147015000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:147012400-147015000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:147012400-147015200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:147012400-147015200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:147012400-147015200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:147012600-147013400	Active TSS	Brain Germinal Matrix	brain
17	chr1:147012600-147014200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:147012600-147014200	Active TSS	Brain Substantia Nigra	brain
19	chr1:147012600-147014400	Active TSS	Left Ventricle	heart
20	chr1:147012600-147014400	Active TSS	Lung	lung
21	chr1:147012600-147014400	Active TSS	Psoas Muscle	Psoas
22	chr1:147012600-147014600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:147012600-147014600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:147012600-147014600	Active TSS	Right Ventricle	heart
25	chr1:147012600-147014800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:147012600-147015200	Active TSS	Ovary	ovary
27	chr1:147012800-147013400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:147012800-147013400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:147012800-147013400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:147012800-147013400	Active TSS	Liver	Liver
31	chr1:147012800-147013400	Active TSS	HSMM	muscle
32	chr1:147012800-147013400	Active TSS	HSMMtube	muscle
33	chr1:147012800-147013600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:147012800-147013800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr1:147012800-147013800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:147012800-147013800	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:147012800-147013800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr1:147012800-147013800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:147012800-147013800	Active TSS	Fetal Brain Female	brain
40	chr1:147012800-147013800	Active TSS	Pancreas	Pancrea
41	chr1:147012800-147013800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:147012800-147013800	Active TSS	Stomach Mucosa	stomach
43	chr1:147012800-147013800	Active TSS	GM12878-XiMat	blood
44	chr1:147012800-147014000	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:147012800-147014000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:147012800-147014000	Active TSS	Duodenum Mucosa	Duodenum
47	chr1:147012800-147014000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:147012800-147014000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:147012800-147014200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:147012800-147014200	Active TSS	Fetal Heart	heart

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