Variant report

Variant	rs12061420
Chromosome Location	chr1:247088428-247088429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247070542..247073488-chr1:247087102..247088901,2	K562	blood:
2	chr1:247071846..247074365-chr1:247086927..247089836,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10924871	0.86[AFR][1000 genomes]
rs10924877	1.00[AMR][1000 genomes]
rs10924878	1.00[AMR][1000 genomes]
rs11800375	1.00[EUR][1000 genomes]
rs11805816	1.00[EUR][1000 genomes]
rs11806722	1.00[EUR][1000 genomes]
rs11807103	1.00[EUR][1000 genomes]
rs11807233	1.00[EUR][1000 genomes]
rs12059361	1.00[AMR][1000 genomes]
rs12065654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088097	1.00[EUR][1000 genomes]
rs12091757	1.00[EUR][1000 genomes]
rs12092189	1.00[EUR][1000 genomes]
rs12096743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097308	1.00[EUR][1000 genomes]
rs13375472	1.00[EUR][1000 genomes]
rs1472276	1.00[EUR][1000 genomes]
rs2067915	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3007328	1.00[EUR][1000 genomes]
rs59476689	1.00[EUR][1000 genomes]
rs6659764	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6686324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694181	1.00[EUR][1000 genomes]
rs73140244	1.00[EUR][1000 genomes]
rs73142251	1.00[EUR][1000 genomes]
rs73142256	1.00[EUR][1000 genomes]
rs73144222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73146640	0.94[AFR][1000 genomes]
rs73146692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73148612	1.00[EUR][1000 genomes]
rs73148614	1.00[AMR][1000 genomes]
rs7512439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7516596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534805	1.00[EUR][1000 genomes]
rs7535104	1.00[EUR][1000 genomes]
rs7537256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9729188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9887864	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247055400-247089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:247061200-247093000	Weak transcription	Fetal Brain Male	brain
3	chr1:247065600-247088800	Weak transcription	Small Intestine	intestine
4	chr1:247069600-247093400	Weak transcription	Colonic Mucosa	Colon
5	chr1:247069600-247093400	Weak transcription	Esophagus	oesophagus
6	chr1:247069800-247093800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:247070000-247093600	Weak transcription	Aorta	Aorta
8	chr1:247070800-247092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:247071000-247093400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:247072200-247088800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:247073600-247089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:247074200-247093400	Weak transcription	NHLF	lung
13	chr1:247075600-247088800	Weak transcription	Fetal Stomach	stomach
14	chr1:247078400-247093600	Weak transcription	Fetal Kidney	kidney
15	chr1:247078600-247089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:247078600-247093400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:247078800-247093400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:247079200-247089000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:247080400-247093400	Weak transcription	Stomach Mucosa	stomach
20	chr1:247080800-247088800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:247080800-247089800	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:247080800-247092000	Weak transcription	NHEK	skin
23	chr1:247081000-247088800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:247081000-247088800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:247081000-247088800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:247081000-247089000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:247081000-247089000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:247081000-247089000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:247081000-247089400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:247081000-247092400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:247081000-247093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:247081000-247093400	Weak transcription	HSMMtube	muscle
33	chr1:247081200-247088800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:247081200-247089000	Weak transcription	Thymus	Thymus
35	chr1:247081200-247089000	Weak transcription	HMEC	breast
36	chr1:247081200-247093400	Weak transcription	NH-A	brain
37	chr1:247081400-247088800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:247082000-247088600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:247082000-247089000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:247082000-247089000	Weak transcription	Fetal Thymus	thymus
41	chr1:247082000-247089400	Weak transcription	Primary B cells from cord blood	blood
42	chr1:247082400-247092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:247082800-247089400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:247083200-247089400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:247083600-247088800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:247083800-247088800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:247084400-247089400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:247085000-247089800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:247085200-247089800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:247085400-247088800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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