Variant report

Variant	rs1344
Chromosome Location	chr1:147119273-147119274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:147119055..147120579-chr1:147144435..147146976,2	MCF-7	breast:
2	chr1:147112511..147115637-chr1:147115937..147121176,5	MCF-7	breast:
3	chr1:147119265..147120096-chr1:147362380..147362969,2	MCF-7	breast:
4	chr1:147113863..147119678-chr1:147120238..147124077,6	K562	blood:
5	chr1:147117692..147123079-chr1:147140177..147144336,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10494247	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]
rs10900387	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1344	POLR3C	cis	cerebellum	SCAN
rs1344	ACP6	cis	Muscle Skeletal	GTEx
rs1344	ACP6	cis	Thyroid	GTEx
rs1344	ACP6	cis	multi-tissue	Pritchard
rs1344	ACP6	cis	Liver	GTEx
rs1344	ACP6	cis	Esophagus Muscularis	GTEx
rs1344	ACP6	Cis_1M	lymphoblastoid	RTeQTL
rs1344	ACP6	cis	brain	seeQTL
rs1344	ACP6	cis	Heart Left Ventricle	GTEx
rs1344	ACP6	cis	lymphoblastoid	seeQTL
rs1344	ACP6	cis	parietal	SCAN
rs1344	ACP6	cis	Artery Tibial	GTEx
rs1344	ACP6	cis	Brain Pons	GTEx
rs1344	ACP6	trans	brain	seeQTL
rs1344	ACP6	cis	Stomach	GTEx
rs1344	ACP6	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr1:147096600-147122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:147096800-147119400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:147096800-147119400	Weak transcription	Aorta	Aorta
5	chr1:147096800-147119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:147096800-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:147096800-147119600	Weak transcription	Gastric	stomach
8	chr1:147096800-147119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:147096800-147119800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:147097600-147130000	Weak transcription	Stomach Mucosa	stomach
11	chr1:147097800-147119800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:147097800-147124000	Weak transcription	Small Intestine	intestine
13	chr1:147098000-147119800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:147102800-147120800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:147109400-147124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:147111000-147128400	Weak transcription	HUVEC	blood vessel
17	chr1:147112600-147119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:147112600-147124000	Weak transcription	HSMMtube	muscle
19	chr1:147112800-147122200	Weak transcription	Psoas Muscle	Psoas
20	chr1:147113000-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:147113000-147136200	Weak transcription	NH-A	brain
22	chr1:147113000-147141400	Weak transcription	Fetal Brain Male	brain
23	chr1:147113200-147122600	Weak transcription	HMEC	breast
24	chr1:147113200-147130800	Weak transcription	NHEK	skin
25	chr1:147113400-147119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:147113400-147119600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:147113400-147121800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:147113400-147122400	Weak transcription	Fetal Lung	lung
29	chr1:147113600-147119400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:147113600-147121800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:147113800-147119600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:147113800-147119800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:147113800-147119800	Weak transcription	Placenta	Placenta
34	chr1:147113800-147123600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:147113800-147126200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:147114000-147119400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:147114000-147120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:147114000-147121000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:147114000-147121600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:147114000-147122200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:147114000-147122800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:147114000-147141000	Weak transcription	Osteobl	bone
43	chr1:147114200-147119600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:147114200-147119800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:147114200-147133800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:147114400-147124800	Strong transcription	Liver	Liver
47	chr1:147114600-147119400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:147115000-147122000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:147115200-147119400	Weak transcription	Thymus	Thymus
50	chr1:147115400-147119600	Weak transcription	Esophagus	oesophagus

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