Variant report

Variant	rs17075907
Chromosome Location	chr13:52305464-52305465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52025570..52029179-chr13:52303526..52308236,11	MCF-7	breast:
2	chr13:52300204..52302832-chr13:52303921..52305515,2	MCF-7	breast:
3	chr13:52023100..52029112-chr13:52304112..52310087,18	MCF-7	breast:
4	chr13:52158523..52160534-chr13:52305074..52307516,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000224892	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1060562	0.86[ASN][1000 genomes]
rs12146894	0.86[ASN][1000 genomes]
rs12427748	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1475195	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17532412	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17597531	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1885854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296028	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296029	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780461	0.82[EUR][1000 genomes]
rs2897944	0.85[ASN][1000 genomes]
rs3908968	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555048	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs483879	1.00[AFR][1000 genomes]
rs488261	1.00[AFR][1000 genomes]
rs491103	0.80[EUR][1000 genomes]
rs60757273	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526783	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9526786	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9526788	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526793	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535714	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9535715	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9535717	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535722	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535735	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535738	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535739	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535744	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535747	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535748	0.85[ASN][1000 genomes]
rs9535749	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535750	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535753	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535756	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:52288400-52322200	Weak transcription	K562	blood
3	chr13:52289400-52305800	Weak transcription	Fetal Kidney	kidney
4	chr13:52290000-52307600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:52293600-52307600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:52296000-52307600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
8	chr13:52297000-52311800	Weak transcription	GM12878-XiMat	blood
9	chr13:52297400-52305800	Strong transcription	Primary B cells from cord blood	blood
10	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
11	chr13:52298400-52307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:52300200-52306400	Enhancers	Liver	Liver
13	chr13:52300200-52311800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:52300600-52307000	Strong transcription	Primary T cells from cord blood	blood
16	chr13:52300600-52316000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr13:52301600-52306200	Enhancers	Brain Substantia Nigra	brain
19	chr13:52301800-52306000	Enhancers	Pancreas	Pancrea
20	chr13:52301800-52306200	Enhancers	Brain Hippocampus Middle	brain
21	chr13:52301800-52306400	Enhancers	Brain Anterior Caudate	brain
22	chr13:52302000-52306000	Enhancers	Fetal Lung	lung
23	chr13:52302200-52314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:52302400-52307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:52302400-52313000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr13:52302600-52313800	Weak transcription	Dnd41	blood
27	chr13:52302800-52313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:52302800-52313200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr13:52303000-52305600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr13:52303000-52306000	Enhancers	Fetal Muscle Leg	muscle
31	chr13:52303000-52306000	Enhancers	NHLF	lung
32	chr13:52303200-52307000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:52303200-52307400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr13:52303400-52306000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52303400-52307200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr13:52303400-52315000	Weak transcription	Fetal Thymus	thymus
37	chr13:52303600-52305800	Enhancers	Stomach Mucosa	stomach
38	chr13:52303600-52306400	Enhancers	Aorta	Aorta
39	chr13:52303600-52306400	Enhancers	Fetal Intestine Large	intestine
40	chr13:52303800-52305600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr13:52303800-52307600	Weak transcription	Brain Angular Gyrus	brain
42	chr13:52303800-52313600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr13:52304000-52306200	Enhancers	HUVEC	blood vessel
44	chr13:52304000-52320400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:52304400-52305600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:52304400-52305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr13:52304400-52306000	Enhancers	Right Atrium	heart
48	chr13:52304400-52306000	Enhancers	Right Ventricle	heart
49	chr13:52304400-52306000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr13:52304400-52306200	Enhancers	A549	lung

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