Variant report

Variant	rs16979703
Chromosome Location	chr19:45653752-45653753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45652567..45654233-chr19:45681921..45683559,2	MCF-7	breast:
2	chr19:45640475..45642060-chr19:45652557..45654572,2	MCF-7	breast:
3	chr19:45648191..45651318-chr19:45652739..45655136,4	MCF-7	breast:
4	chr19:45651718..45653898-chr19:45656029..45658572,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKPD1-2	chr19:45653008-45653863	ENSG00000267037.1

Variant related genes	Relation type
ENSG00000189114	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000179846	Chromatin interaction
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16979659	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs35527954	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs56213215	1.00[AMR][1000 genomes]
rs56405239	1.00[AMR][1000 genomes]
rs57454146	1.00[AMR][1000 genomes]
rs58584483	1.00[AMR][1000 genomes]
rs60509946	1.00[AMR][1000 genomes]
rs60530130	1.00[AMR][1000 genomes]
rs73939603	1.00[AMR][1000 genomes]
rs73939647	1.00[AMR][1000 genomes]
rs73939649	1.00[AMR][1000 genomes]
rs73941103	1.00[AMR][1000 genomes]
rs73941104	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45625000-45654200	Weak transcription	NHDF-Ad	bronchial
2	chr19:45627600-45655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:45633600-45655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:45639800-45656800	Weak transcription	K562	blood
5	chr19:45640000-45653800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:45640000-45654400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:45640400-45655000	Weak transcription	Fetal Heart	heart
8	chr19:45641400-45654600	Weak transcription	HSMM	muscle
9	chr19:45641600-45654000	Weak transcription	HSMMtube	muscle
10	chr19:45641800-45653800	Weak transcription	Stomach Mucosa	stomach
11	chr19:45642000-45655200	Weak transcription	GM12878-XiMat	blood
12	chr19:45642000-45655400	Weak transcription	Right Atrium	heart
13	chr19:45643000-45654200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:45643000-45654200	Strong transcription	Gastric	stomach
15	chr19:45643600-45654000	Weak transcription	HMEC	breast
16	chr19:45644600-45653800	Weak transcription	HepG2	liver
17	chr19:45646000-45655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:45646600-45654000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:45646600-45655000	Weak transcription	Primary B cells from cord blood	blood
20	chr19:45646800-45655000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:45647000-45654400	Weak transcription	Brain Substantia Nigra	brain
22	chr19:45647000-45654600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:45647000-45655400	Weak transcription	Left Ventricle	heart
24	chr19:45647200-45654200	Weak transcription	Fetal Lung	lung
25	chr19:45648600-45654800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:45649600-45654200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:45649800-45654400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:45649800-45654800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:45650000-45654200	Weak transcription	NHEK	skin
30	chr19:45650000-45655200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:45650000-45655400	Weak transcription	Liver	Liver
32	chr19:45650000-45655800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:45650200-45653800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:45650200-45653800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:45650200-45654400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:45650200-45654400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:45650200-45654800	Weak transcription	Osteobl	bone
38	chr19:45650200-45655200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:45650200-45655600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr19:45650400-45654000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:45650400-45654200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr19:45650600-45653800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:45650600-45654200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:45650600-45654600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:45650800-45653800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:45650800-45654000	Weak transcription	Placenta	Placenta
47	chr19:45650800-45654600	Weak transcription	Brain Anterior Caudate	brain
48	chr19:45650800-45654800	Weak transcription	Brain Hippocampus Middle	brain
49	chr19:45650800-45655000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr19:45650800-45655200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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