Variant report

Variant	rs16973959
Chromosome Location	chr19:40498011-40498012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40497431..40499811-chr19:40501721..40503252,2	MCF-7	breast:
2	chr19:40497251..40499736-chr19:40500341..40503901,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF780B-2	chr19:40497983-40502942	NONHSAT066331

Variant related genes	Relation type
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10421829	1.00[CHB][hapmap]
rs173062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234329	1.00[CHB][hapmap]
rs234335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	1.00[ASN][1000 genomes]
rs234337	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234338	1.00[CHB][hapmap]
rs234344	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	1.00[ASN][1000 genomes]
rs234347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	1.00[ASN][1000 genomes]
rs234366	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234373	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531363	1.00[CHB][hapmap]
rs2542325	1.00[ASN][1000 genomes]
rs2542328	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337796	1.00[CHB][hapmap]
rs376630	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378554	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399405	1.00[CHB][hapmap]
rs420413	1.00[CHB][hapmap]
rs512360	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413463	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255173	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	1.00[CHB][hapmap]
rs7260610	1.00[CHB][hapmap]
rs8113194	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913212	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40477800-40501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40478600-40501800	Weak transcription	Right Atrium	heart
3	chr19:40487200-40499600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:40487600-40501800	Weak transcription	Right Ventricle	heart
5	chr19:40488200-40499600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:40488200-40501800	Weak transcription	Esophagus	oesophagus
7	chr19:40488400-40501800	Weak transcription	Left Ventricle	heart
8	chr19:40488800-40501800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:40489000-40501600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:40489600-40500200	Weak transcription	Fetal Kidney	kidney
11	chr19:40490200-40499600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:40490200-40499600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:40490200-40499800	Weak transcription	Lung	lung
14	chr19:40490200-40501600	Weak transcription	HSMM	muscle
15	chr19:40490200-40501600	Weak transcription	Osteobl	bone
16	chr19:40490200-40501800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:40490200-40501800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:40490200-40502400	Weak transcription	Aorta	Aorta
19	chr19:40490400-40499600	Weak transcription	Fetal Thymus	thymus
20	chr19:40490400-40501800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:40491000-40502200	Weak transcription	Ovary	ovary
22	chr19:40493000-40501800	Weak transcription	Brain Angular Gyrus	brain
23	chr19:40493000-40501800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:40493200-40501800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:40493400-40499600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:40493400-40499800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:40493400-40501800	Weak transcription	Psoas Muscle	Psoas
28	chr19:40493600-40499400	Weak transcription	Primary B cells from cord blood	blood
29	chr19:40493600-40501000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:40493600-40501600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:40493800-40498600	Weak transcription	Fetal Brain Female	brain
32	chr19:40494400-40498800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:40494400-40499200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:40494400-40501800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:40494800-40498800	Weak transcription	Fetal Stomach	stomach
36	chr19:40494800-40499000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr19:40494800-40499600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:40495400-40501800	Weak transcription	Adipose Nuclei	Adipose
39	chr19:40495600-40499200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr19:40495600-40501800	Weak transcription	HSMMtube	muscle
41	chr19:40496200-40499200	Weak transcription	Dnd41	blood
42	chr19:40496200-40501800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:40496600-40502200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:40496800-40498400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr19:40497200-40499200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:40497400-40498200	Genic enhancers	Primary T cells from cord blood	blood
47	chr19:40497600-40500600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:40497600-40501400	Weak transcription	Pancreas	Pancrea
49	chr19:40497600-40501600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr19:40497800-40499000	Weak transcription	Fetal Intestine Small	intestine

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