Variant report

Variant	rs1925730
Chromosome Location	chr1:228666410-228666411
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	chr1:228665457..228668027-chr1:228670645..228673009,2	MCF-7	breast:
2	chr1:228644574..228646837-chr1:228664385..228666953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1007686	0.85[CEU][hapmap]
rs10753451	0.80[EUR][1000 genomes]
rs10799479	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10916313	0.87[CEU][hapmap]
rs10916317	0.85[CEU][hapmap]
rs10916329	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12060006	0.87[EUR][1000 genomes]
rs12542	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1925714	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4147255	0.86[CEU][hapmap]
rs4653551	0.85[CEU][hapmap]
rs4653554	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4653966	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653968	0.96[EUR][1000 genomes]
rs4653969	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs4653970	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6426503	0.85[CEU][hapmap]
rs6426505	0.90[EUR][1000 genomes]
rs6669744	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6678145	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7415895	0.84[CEU][hapmap]
rs7524236	0.85[CEU][hapmap]
rs7529055	0.85[CEU][hapmap]
rs7536593	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	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
12	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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228661400-228666600	Weak transcription	HUVEC	blood vessel
2	chr1:228663000-228668000	Enhancers	K562	blood
3	chr1:228663600-228666600	Weak transcription	HepG2	liver
4	chr1:228663800-228666600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:228664600-228666600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:228664800-228666600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:228665000-228666600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:228665000-228667600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:228665000-228667800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:228665000-228668000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:228665200-228666600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:228665400-228666600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:228665400-228666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:228665600-228667400	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:228665800-228666600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:228666000-228666800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:228666000-228667400	Enhancers	Spleen	Spleen
18	chr1:228666000-228667600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:228666000-228667600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:228666000-228667800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:228666000-228668000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:228666000-228668000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:228666000-228668000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:228666000-228668000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:228666200-228666600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:228666200-228667400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:228666200-228667600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:228666400-228666600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:228666400-228666600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:228666400-228666600	Enhancers	GM12878-XiMat	blood
31	chr1:228666400-228666800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:228666400-228667000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:228666400-228667400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:228666400-228667400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:228666400-228667600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:228666400-228667600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:228666400-228667600	Enhancers	Primary T helper cells PMA-I stimulated	--

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