Variant report

Variant	rs12026004
Chromosome Location	chr1:228678927-228678928
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	POLR2A	chr1:228675579-228678949	K562	blood:	n/a	n/a
2	POLR2A	chr1:228678692-228678958	HepG2	liver:	n/a	n/a
3	JUN	chr1:228672601-228678958	K562	blood:	n/a	chr1:228677697-228677705 chr1:228678292-228678303

No.	Distal block	Cell Line	Cell type
1	chr1:228678547..228680659-chr1:228683651..228685431,2	MCF-7	breast:
2	chr1:228677727..228683972-chr1:228696742..228702359,8	K562	blood:
3	chr1:228677081..228680251-chr1:228681214..228683953,4	MCF-7	breast:
4	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
5	chr1:228678361..228680041-chr1:228700662..228702359,2	K562	blood:

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000168159	Chromatin interaction
ENSG00000215811	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1011878	0.80[JPT][hapmap]
rs1011879	0.81[JPT][hapmap]
rs10916331	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12076802	0.84[AFR][1000 genomes]
rs16848741	0.82[YRI][hapmap]
rs3795816	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4271208	0.85[EUR][1000 genomes]
rs6684355	0.97[EUR][1000 genomes]
rs6688436	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs71650387	0.82[ASN][1000 genomes]
rs9287013	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228675400-228684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228676400-228683000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:228676400-228684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:228676400-228685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228676400-228688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:228676600-228680400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:228676600-228688800	Weak transcription	HUVEC	blood vessel
8	chr1:228676800-228679400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:228676800-228679600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:228676800-228683400	Strong transcription	NHLF	lung
11	chr1:228676800-228683600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:228676800-228685600	Strong transcription	Primary T cells from cord blood	blood
13	chr1:228676800-228686000	Strong transcription	Fetal Intestine Small	intestine
14	chr1:228676800-228688400	Weak transcription	Stomach Mucosa	stomach
15	chr1:228676800-228688600	Weak transcription	Small Intestine	intestine
16	chr1:228677000-228679000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:228677000-228679000	Strong transcription	Fetal Kidney	kidney
18	chr1:228677000-228681400	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr1:228677000-228682400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:228677000-228683800	Strong transcription	Fetal Thymus	thymus
21	chr1:228677000-228685200	Strong transcription	Fetal Lung	lung
22	chr1:228677000-228686000	Strong transcription	Fetal Stomach	stomach
23	chr1:228677200-228679000	Strong transcription	Thymus	Thymus
24	chr1:228677200-228679600	Strong transcription	Primary B cells from cord blood	blood
25	chr1:228677200-228679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:228677200-228683800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:228677200-228683800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:228677200-228684000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:228677200-228684000	Strong transcription	Fetal Intestine Large	intestine
30	chr1:228677200-228684000	Strong transcription	Placenta	Placenta
31	chr1:228677400-228679000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:228677400-228679400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:228677400-228679800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:228677400-228680000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:228677400-228680600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:228677400-228682400	Strong transcription	HSMM	muscle
37	chr1:228677400-228683400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:228677400-228683600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr1:228677400-228683800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:228677400-228684000	Strong transcription	Osteobl	bone
41	chr1:228677400-228685400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:228677400-228685800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:228677400-228686000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:228677600-228679000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:228677600-228679400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:228677600-228683000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:228677600-228686000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:228677600-228686000	Strong transcription	Ovary	ovary
49	chr1:228677800-228679000	Strong transcription	Aorta	Aorta
50	chr1:228677800-228679000	Enhancers	Right Atrium	heart

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