Variant report

Variant	rs1506680
Chromosome Location	chr12:45268136-45268137
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	chr12:44408858..44409800-chr12:45267480..45268238,2	MCF-7	breast:
2	chr12:45168304..45169119-chr12:45267170..45268311,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10506258	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10785535	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10785538	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10785540	0.83[EUR][1000 genomes]
rs11504491	0.82[AMR][1000 genomes]
rs11524561	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11615964	0.84[ASN][1000 genomes]
rs1376126	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1395397	0.85[EUR][1000 genomes]
rs1506676	0.81[ASN][1000 genomes]
rs1506678	0.81[ASN][1000 genomes]
rs1506679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605296	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1605297	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1605298	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1857927	0.85[EUR][1000 genomes]
rs1876241	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2055677	0.85[EUR][1000 genomes]
rs2258058	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2408084	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2408085	0.88[AMR][1000 genomes]
rs2465108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465109	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2465110	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2658948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2658951	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2658954	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2658957	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2658959	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2658965	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2658966	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710453	0.85[EUR][1000 genomes]
rs2710457	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710459	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710461	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2939697	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2939698	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238095	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4300447	0.83[EUR][1000 genomes]
rs4415832	0.82[AMR][1000 genomes]
rs4499065	0.90[AMR][1000 genomes]
rs4768075	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55741117	0.85[EUR][1000 genomes]
rs7295923	0.85[ASN][1000 genomes]
rs7304472	0.84[ASN][1000 genomes]
rs7312377	0.88[ASN][1000 genomes]
rs7952764	0.81[ASN][1000 genomes]
rs7971834	0.82[AMR][1000 genomes]
rs7973268	0.85[AMR][1000 genomes]
rs7979717	0.81[ASN][1000 genomes]
rs884259	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs884260	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
2	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45263000-45269000	Active TSS	Fetal Brain Female	brain
2	chr12:45264800-45271200	Active TSS	Fetal Brain Male	brain
3	chr12:45266000-45270600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
4	chr12:45266400-45268600	Active TSS	Brain Angular Gyrus	brain
5	chr12:45266400-45269200	Active TSS	Brain Anterior Caudate	brain
6	chr12:45266800-45268800	Active TSS	Brain Hippocampus Middle	brain
7	chr12:45266800-45269200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:45266800-45270800	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr12:45267000-45268800	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr12:45267000-45269200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr12:45267200-45268400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:45267200-45271000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:45267200-45271400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:45267400-45268200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:45267800-45268200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:45267800-45268400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:45267800-45268600	Active TSS	Primary T cells fromperipheralblood	blood
18	chr12:45267800-45268800	Active TSS	Brain Germinal Matrix	brain
19	chr12:45267800-45271000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
20	chr12:45268000-45268200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr12:45268000-45268200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:45268000-45268200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr12:45268000-45268200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:45268000-45268200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
25	chr12:45268000-45268200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:45268000-45268200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:45268000-45268200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:45268000-45268200	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr12:45268000-45268200	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr12:45268000-45268400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
31	chr12:45268000-45268400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:45268000-45268600	Active TSS	Brain Cingulate Gyrus	brain
33	chr12:45268000-45268600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
34	chr12:45268000-45268800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr12:45268000-45268800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
36	chr12:45268000-45268800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr12:45268000-45270000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr12:45268000-45270800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:45268000-45270800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:45268000-45271000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:45268000-45271200	Active TSS	H9 Cell Line	embryonic stem cell

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