Variant report

Variant	rs3806218
Chromosome Location	chr1:147011783-147011784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:147011533-147014443	H1-neurons	neurons:	n/a	chr1:147012316-147012336
2	FOSL1	chr1:147010671-147011838	HCT-116	colon:	n/a	chr1:147011024-147011034 chr1:147011024-147011034 chr1:147011052-147011062 chr1:147011024-147011034 chr1:147011051-147011062 chr1:147011557-147011565 chr1:147011053-147011061 chr1:147011023-147011035 chr1:147011024-147011034 chr1:147011052-147011062 chr1:147011049-147011060 chr1:147011025-147011034 chr1:147011023-147011034 chr1:147011051-147011063
3	MAZ	chr1:147011416-147012354	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:147011744..147014234-chr1:147070783..147073063,3	K562	blood:
2	chr1:147011744..147014234-chr1:147070783..147072314,2	K562	blood:
3	chr1:147009715..147011902-chr1:147032676..147034909,2	MCF-7	breast:
4	chr1:147010058..147012645-chr11:64784779..64787267,2	MCF-7	breast:
5	chr1:147008733..147014706-chr1:147069097..147075030,9	MCF-7	breast:
6	chr1:147010483..147014086-chr1:147140786..147143809,3	MCF-7	breast:

Variant related genes	Relation type
BCL9	TF binding region
ENSG00000116128	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1015235	0.80[JPT][hapmap]
rs10793689	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10900376	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]
rs11583944	0.85[JPT][hapmap]
rs12119310	0.87[AFR][1000 genomes]
rs12127408	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2132440	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2353544	0.85[JPT][hapmap]
rs4950460	0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666569	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666306	0.80[CHB][hapmap];0.90[JPT][hapmap]

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	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
22	nsv946307	chr1:146982909-147012496	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3806218	PGAP1	trans	parietal	SCAN
rs3806218	ACP6	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147006600-147012600	Weak transcription	Pancreas	Pancrea
2	chr1:147008400-147012400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:147009800-147012200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:147009800-147012400	Enhancers	Fetal Heart	heart
5	chr1:147010000-147012200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:147010000-147012400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:147010000-147012400	Enhancers	NHLF	lung
8	chr1:147010000-147012600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:147010000-147012600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:147010000-147012600	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:147010000-147012600	Enhancers	NHDF-Ad	bronchial
12	chr1:147010000-147013200	Enhancers	Hela-S3	cervix
13	chr1:147010200-147011800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:147010200-147011800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:147010200-147011800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:147010200-147011800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:147010200-147011800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:147010200-147011800	Enhancers	A549	lung
19	chr1:147010200-147012000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:147010200-147012000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:147010200-147012000	Enhancers	Small Intestine	intestine
22	chr1:147010200-147012200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:147010200-147012200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:147010200-147012200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:147010200-147012400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:147010200-147012400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:147010200-147012400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:147010200-147012400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr1:147010200-147012400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:147010200-147012400	Enhancers	Fetal Thymus	thymus
31	chr1:147010200-147012600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:147010200-147012600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:147010200-147012600	Enhancers	Fetal Intestine Large	intestine
34	chr1:147010200-147012600	Enhancers	HSMMtube	muscle
35	chr1:147010200-147012600	Enhancers	NH-A	brain
36	chr1:147010200-147012600	Enhancers	Osteobl	bone
37	chr1:147010400-147011800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:147010400-147012200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:147010400-147012200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:147010400-147012400	Enhancers	Fetal Intestine Small	intestine
41	chr1:147010400-147012400	Enhancers	Fetal Stomach	stomach
42	chr1:147010400-147012400	Enhancers	Rectal Smooth Muscle	rectum
43	chr1:147010400-147012600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:147010400-147012600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:147010400-147012600	Enhancers	Fetal Lung	lung
46	chr1:147010400-147012600	Enhancers	HUVEC	blood vessel
47	chr1:147010600-147011800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:147010600-147012000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:147010600-147012000	Enhancers	Fetal Kidney	kidney
50	chr1:147010600-147012400	Enhancers	H1 Cell Line	embryonic stem cell

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