Variant report

Variant	rs59438946
Chromosome Location	chr1:147117540-147117541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:147112511..147115637-chr1:147115937..147121176,5	MCF-7	breast:
2	chr1:147115260..147119161-chr1:147125330..147128205,3	MCF-7	breast:
3	chr1:147115798..147117787-chr1:147134133..147136995,2	K562	blood:
4	chr1:147113863..147119678-chr1:147120238..147124077,6	K562	blood:

Variant related genes	Relation type
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56936807	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57359024	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57463094	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57515690	1.00[ASN][1000 genomes]
rs58826432	0.81[AFR][1000 genomes]
rs61657066	0.82[AFR][1000 genomes];1.00[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

No data

Chromatin state (count:112 , 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	chr1:147092800-147117600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:147096600-147122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:147096800-147119400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:147096800-147119400	Weak transcription	Aorta	Aorta
6	chr1:147096800-147119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:147096800-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:147096800-147119600	Weak transcription	Gastric	stomach
9	chr1:147096800-147119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:147096800-147119800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:147097600-147130000	Weak transcription	Stomach Mucosa	stomach
12	chr1:147097800-147119800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:147097800-147124000	Weak transcription	Small Intestine	intestine
14	chr1:147098000-147119800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:147099400-147119200	Weak transcription	Fetal Intestine Large	intestine
16	chr1:147102800-147120800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:147104800-147119200	Weak transcription	Pancreas	Pancrea
18	chr1:147107400-147118200	Weak transcription	Primary B cells from cord blood	blood
19	chr1:147109400-147124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:147111000-147117600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:147111000-147128400	Weak transcription	HUVEC	blood vessel
22	chr1:147112600-147119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:147112600-147124000	Weak transcription	HSMMtube	muscle
24	chr1:147112800-147122200	Weak transcription	Psoas Muscle	Psoas
25	chr1:147113000-147119200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:147113000-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:147113000-147136200	Weak transcription	NH-A	brain
28	chr1:147113000-147141400	Weak transcription	Fetal Brain Male	brain
29	chr1:147113200-147122600	Weak transcription	HMEC	breast
30	chr1:147113200-147130800	Weak transcription	NHEK	skin
31	chr1:147113400-147118600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:147113400-147119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:147113400-147119600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:147113400-147121800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:147113400-147122400	Weak transcription	Fetal Lung	lung
36	chr1:147113600-147118800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:147113600-147119000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:147113600-147119400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:147113600-147121800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:147113800-147117600	Weak transcription	Dnd41	blood
41	chr1:147113800-147118000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:147113800-147119600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:147113800-147119800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:147113800-147119800	Weak transcription	Placenta	Placenta
45	chr1:147113800-147123600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:147113800-147126200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:147114000-147118200	Weak transcription	Fetal Heart	heart
48	chr1:147114000-147119400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:147114000-147120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:147114000-147121000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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