Variant report

Variant	rs16949427
Chromosome Location	chr17:45992916-45992917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45981534..45985192-chr17:45991810..45993717,3	MCF-7	breast:
2	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
3	chr17:45978419..45981029-chr17:45992865..45995390,2	MCF-7	breast:
4	chr17:45992709..45994396-chr17:45996856..45998957,2	MCF-7	breast:
5	chr17:45991986..45994660-chr17:45998582..46001397,3	K562	blood:
6	chr17:45991270..45994231-chr17:46005074..46007219,2	K562	blood:
7	chr17:45971250..45975448-chr17:45992732..45995737,5	MCF-7	breast:
8	chr17:45992911..45994770-chr17:46006904..46009157,2	K562	blood:
9	chr17:45991808..45994318-chr17:46045941..46048411,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1133221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16949270	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16949296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16949651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17616799	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs1986694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2325750	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2525105	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs3764393	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4450442	0.82[CHB][hapmap]
rs55956628	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56006220	0.91[ASN][1000 genomes]
rs73323310	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9944405	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
3	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
4	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
5	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:45980200-46001800	Weak transcription	K562	blood
10	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
14	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:45982800-45993000	Weak transcription	NHEK	skin
16	chr17:45983000-45993800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr17:45983200-45993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:45983200-45995200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr17:45983200-45995200	Weak transcription	HUVEC	blood vessel
22	chr17:45983200-46000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:45983200-46001200	Weak transcription	A549	lung
24	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
25	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
26	chr17:45984000-45993600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:45984200-45993200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:45984200-46000600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:45984400-45993400	Weak transcription	Pancreas	Pancrea
30	chr17:45984600-45993200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:45984600-45994200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr17:45985600-45993200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:45985600-45993400	Weak transcription	Fetal Lung	lung
34	chr17:45985600-45993800	Weak transcription	NHLF	lung
35	chr17:45985600-46000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr17:45985800-45993000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:45985800-45993800	Weak transcription	Brain Angular Gyrus	brain
38	chr17:45985800-45993800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr17:45986000-45993000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr17:45986000-46000400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:45986600-45994000	Weak transcription	Osteobl	bone
42	chr17:45986800-45993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:45987000-45993200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:45987000-46000200	Weak transcription	Aorta	Aorta
45	chr17:45987200-45997000	Weak transcription	HepG2	liver
46	chr17:45988400-45993000	Weak transcription	Primary T cells from cord blood	blood
47	chr17:45988400-46000400	Weak transcription	Brain Substantia Nigra	brain
48	chr17:45988400-46000600	Weak transcription	HSMM	muscle
49	chr17:45988600-45993600	Weak transcription	Liver	Liver
50	chr17:45990000-45993000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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