Variant report

Variant	rs1264448
Chromosome Location	chr6:30542999-30543000
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	chr6:30541727..30544215-chr6:30582444..30584510,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1058318	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264432	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264437	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1264438	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264439	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264440	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1264456	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1362119	0.84[EUR][1000 genomes]
rs1468079	0.83[EUR][1000 genomes]
rs2023608	0.81[EUR][1000 genomes]
rs2023609	0.81[EUR][1000 genomes]
rs2074503	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074504	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074505	0.84[EUR][1000 genomes]
rs2252745	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2269709	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2269710	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2429655	0.81[EUR][1000 genomes]
rs2516639	0.85[EUR][1000 genomes]
rs2516641	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516642	0.85[EUR][1000 genomes]
rs2516643	0.85[EUR][1000 genomes]
rs2516644	0.84[EUR][1000 genomes]
rs2516646	0.83[EUR][1000 genomes]
rs2516648	0.81[EUR][1000 genomes]
rs2516649	0.83[EUR][1000 genomes]
rs2516656	0.81[EUR][1000 genomes]
rs2516662	0.81[EUR][1000 genomes]
rs2524221	0.83[EUR][1000 genomes]
rs2524223	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2524224	0.82[EUR][1000 genomes]
rs2524226	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2534802	0.80[EUR][1000 genomes]
rs2534803	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534804	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534805	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534807	0.81[EUR][1000 genomes]
rs2534808	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2534810	0.80[EUR][1000 genomes]
rs2534813	0.81[EUR][1000 genomes]
rs2534814	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2534815	0.84[EUR][1000 genomes]
rs2534817	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534820	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2534821	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2534823	0.82[EUR][1000 genomes]
rs2534824	0.82[EUR][1000 genomes]
rs2534825	0.80[EUR][1000 genomes]
rs2844713	0.83[EUR][1000 genomes]
rs2844714	0.83[EUR][1000 genomes]
rs2844715	0.83[EUR][1000 genomes]
rs2844717	0.81[EUR][1000 genomes]
rs2844718	0.82[EUR][1000 genomes]
rs2844720	0.81[EUR][1000 genomes]
rs2844723	0.82[EUR][1000 genomes]
rs2844724	0.81[EUR][1000 genomes]
rs3094718	0.84[EUR][1000 genomes]
rs3130039	0.83[EUR][1000 genomes]
rs3130041	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130043	0.83[EUR][1000 genomes]
rs3130045	0.81[EUR][1000 genomes]
rs3130240	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130242	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130243	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130244	0.83[EUR][1000 genomes]
rs3132609	0.84[EUR][1000 genomes]
rs3132612	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3132613	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132614	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262082	0.81[EUR][1000 genomes]
rs9262118	0.83[EUR][1000 genomes]
rs975195	0.81[EUR][1000 genomes]
rs996588	0.82[EUR][1000 genomes]
rs996589	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS 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 miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30540000-30544400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30540000-30544400	Weak transcription	Ovary	ovary
3	chr6:30540000-30545400	Weak transcription	Aorta	Aorta
4	chr6:30540200-30543200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:30540200-30543600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:30540200-30543600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr6:30540200-30544600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30540200-30544600	Weak transcription	Fetal Kidney	kidney
9	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:30540400-30543200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:30540400-30543200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:30540400-30543400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:30540400-30543600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:30540400-30543800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:30540400-30544400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:30540400-30544400	Weak transcription	HSMMtube	muscle
18	chr6:30540400-30563000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:30540600-30543600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:30540800-30543200	Weak transcription	Fetal Lung	lung
21	chr6:30540800-30543800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:30540800-30560800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr6:30540800-30563600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:30540800-30563600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:30540800-30563800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30541000-30543000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:30541000-30543200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:30541000-30543200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:30541000-30543200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:30541000-30543200	Weak transcription	Left Ventricle	heart
31	chr6:30541000-30543200	Weak transcription	Lung	lung
32	chr6:30541000-30543400	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:30541000-30543600	Genic enhancers	HepG2	liver
34	chr6:30541000-30544200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:30541000-30544400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:30541000-30544400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:30541000-30544400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:30541000-30544400	Weak transcription	Psoas Muscle	Psoas
39	chr6:30541000-30544400	Weak transcription	A549	lung
40	chr6:30541000-30544600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:30541000-30544600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:30541000-30544600	Weak transcription	Pancreas	Pancrea
43	chr6:30541000-30545200	Weak transcription	Gastric	stomach
44	chr6:30541000-30545400	Weak transcription	Colonic Mucosa	Colon
45	chr6:30541000-30550400	Weak transcription	Fetal Brain Male	brain
46	chr6:30541200-30543000	Enhancers	Primary T cells from cord blood	blood
47	chr6:30541200-30543200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:30541200-30543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:30541200-30543200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:30541200-30544400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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