Variant report

Variant	rs16945724
Chromosome Location	chr17:60017888-60017889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60003740..60007255-chr17:60016525..60022639,9	MCF-7	breast:
2	chr17:60001930..60007756-chr17:60014153..60029774,25	MCF-7	breast:
3	chr17:60003769..60005746-chr17:60016413..60018003,2	K562	blood:
4	chr17:60008585..60011122-chr17:60017280..60019717,2	MCF-7	breast:
5	chr17:60017040..60020796-chr17:60041060..60043758,3	K562	blood:
6	chr17:60017329..60019880-chr17:60023720..60025773,3	K562	blood:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10221202	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1045196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512491	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12601229	1.00[AFR][1000 genomes]
rs12601523	1.00[AFR][1000 genomes]
rs12603627	0.82[AFR][1000 genomes]
rs12603878	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs12937188	1.00[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16945638	1.00[MKK][hapmap]
rs16945670	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs16945762	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs16945785	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16945823	0.90[CHB][hapmap]
rs2378946	0.82[AFR][1000 genomes]
rs28500646	0.93[ASN][1000 genomes]
rs4280312	0.81[ASN][1000 genomes]
rs72843746	0.82[AFR][1000 genomes]
rs72843758	1.00[AFR][1000 genomes]
rs72843759	1.00[AFR][1000 genomes]
rs72843762	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72843767	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72843769	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72843770	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72843771	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72843772	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72843775	0.94[ASN][1000 genomes]
rs72843778	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72843782	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72843785	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72843788	0.87[ASN][1000 genomes]
rs72843791	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72843793	0.86[ASN][1000 genomes]
rs72843797	0.86[ASN][1000 genomes]
rs753765	1.00[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes]
rs8081200	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9910451	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60005400-60018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:60005800-60022000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:60005800-60022000	Weak transcription	Thymus	Thymus
4	chr17:60005800-60022800	Weak transcription	Brain Angular Gyrus	brain
5	chr17:60006000-60018000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr17:60006000-60018000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:60006000-60018400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:60006000-60018600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr17:60006000-60018600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr17:60006000-60019400	Weak transcription	Hela-S3	cervix
11	chr17:60006000-60019600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr17:60006000-60020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:60006000-60020800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:60006000-60021000	Weak transcription	HMEC	breast
15	chr17:60006000-60021200	Weak transcription	Osteobl	bone
16	chr17:60006000-60021400	Weak transcription	HUVEC	blood vessel
17	chr17:60006000-60022000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:60006000-60022000	Weak transcription	Fetal Brain Female	brain
19	chr17:60006000-60022000	Weak transcription	HSMMtube	muscle
20	chr17:60006000-60022800	Weak transcription	Brain Anterior Caudate	brain
21	chr17:60006000-60023000	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:60006000-60023600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr17:60006200-60018200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:60009800-60018400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:60011000-60018000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr17:60012000-60018600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr17:60012600-60018600	Weak transcription	Liver	Liver
28	chr17:60012800-60023800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:60013200-60021000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:60013400-60018400	Weak transcription	Fetal Stomach	stomach
31	chr17:60013400-60021400	Weak transcription	NHDF-Ad	bronchial
32	chr17:60013800-60021600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:60014200-60018000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:60014200-60021200	Weak transcription	Dnd41	blood
35	chr17:60014200-60030000	Weak transcription	Stomach Mucosa	stomach
36	chr17:60014400-60020400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:60014400-60022000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr17:60014400-60022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:60014600-60024400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:60014800-60018200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr17:60014800-60019200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr17:60014800-60020200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:60014800-60020600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:60014800-60023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr17:60014800-60028000	Weak transcription	Colonic Mucosa	Colon
46	chr17:60015000-60018400	Weak transcription	Placenta	Placenta
47	chr17:60015000-60022800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr17:60015200-60018600	Weak transcription	Fetal Thymus	thymus
49	chr17:60015400-60021200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:60015400-60022200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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