Variant report

Variant	rs251860
Chromosome Location	chr19:39917761-39917762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:50458005..50459649-chr19:39917436..39920368,2	MCF-7	breast:
2	chr19:39911800..39914936-chr19:39915871..39918478,3	MCF-7	breast:
3	chr19:39917343..39919360-chr19:39932932..39935140,2	MCF-7	breast:
4	chr19:39915342..39916957-chr19:39916979..39919704,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLEKHG2-1	chr19:39916575-39919055	ENSG00000269410.1

Variant related genes	Relation type
ENSG00000269410	Chromatin interaction
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10423537	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10424217	0.82[EUR][1000 genomes]
rs1130180	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609112	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12978920	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12978954	0.84[EUR][1000 genomes]
rs12979605	0.81[EUR][1000 genomes]
rs12983040	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1529732	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1560730	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17626	0.85[ASN][1000 genomes]
rs17628	0.85[ASN][1000 genomes]
rs1865091	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865092	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1932	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009970	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060270	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060271	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2116932	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288933	0.84[EUR][1000 genomes]
rs2288934	0.84[EUR][1000 genomes]
rs2304219	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2304221	0.85[EUR][1000 genomes]
rs2353678	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353679	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs251855	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs251856	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs251857	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs251858	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs251859	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28528765	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28637729	0.82[EUR][1000 genomes]
rs28649498	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31726	0.82[ASN][1000 genomes]
rs31727	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs31728	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34918990	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35647910	0.84[EUR][1000 genomes]
rs4390710	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802026	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803237	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803240	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803241	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803242	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4803245	0.84[EUR][1000 genomes]
rs4803246	0.82[EUR][1000 genomes]
rs4803247	0.84[EUR][1000 genomes]
rs480595	0.85[ASN][1000 genomes]
rs480656	0.85[ASN][1000 genomes]
rs481421	0.85[ASN][1000 genomes]
rs504017	0.81[ASN][1000 genomes]
rs566130	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59007555	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs640000	0.85[ASN][1000 genomes]
rs6508862	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6508863	0.84[EUR][1000 genomes]
rs6508864	0.83[EUR][1000 genomes]
rs6508865	0.81[EUR][1000 genomes]
rs651601	0.83[ASN][1000 genomes]
rs686956	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251384	0.83[EUR][1000 genomes]
rs7251652	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7255253	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73035416	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73549933	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8107194	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8107647	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8110134	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110716	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111260	0.83[EUR][1000 genomes]
rs878754	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
3	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
7	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs251860	RPS16	cis	Heart Left Ventricle	GTEx
rs251860	RPS16	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39921000	Weak transcription	Small Intestine	intestine
2	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39905000-39921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39905200-39918800	Weak transcription	Pancreas	Pancrea
5	chr19:39905400-39921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:39905400-39921200	Weak transcription	K562	blood
7	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39905600-39921600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:39905800-39918000	Weak transcription	HepG2	liver
10	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
11	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:39906200-39919000	Weak transcription	HMEC	breast
13	chr19:39906400-39921200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:39907000-39919000	Weak transcription	Right Atrium	heart
15	chr19:39907600-39918200	Weak transcription	Fetal Heart	heart
16	chr19:39907800-39918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:39910000-39918400	Weak transcription	Hela-S3	cervix
18	chr19:39910000-39921000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:39910000-39921200	Weak transcription	NHEK	skin
20	chr19:39910000-39922600	Weak transcription	Liver	Liver
21	chr19:39911400-39923400	Weak transcription	Fetal Brain Male	brain
22	chr19:39913000-39918400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:39913000-39918400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:39913600-39921400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:39913800-39922800	Weak transcription	Psoas Muscle	Psoas
26	chr19:39914000-39921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:39914000-39921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39914400-39918000	Weak transcription	Colonic Mucosa	Colon
29	chr19:39914800-39921600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:39915200-39918400	Weak transcription	Left Ventricle	heart
31	chr19:39915200-39918400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:39915200-39918400	Weak transcription	NHDF-Ad	bronchial
33	chr19:39915200-39918600	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:39915200-39918800	Weak transcription	HUVEC	blood vessel
35	chr19:39915200-39920600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39915200-39921600	Weak transcription	Primary B cells from cord blood	blood
37	chr19:39915200-39921600	Weak transcription	Esophagus	oesophagus
38	chr19:39915400-39918200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:39915400-39918400	Weak transcription	Adipose Nuclei	Adipose
40	chr19:39915400-39918400	Weak transcription	Ovary	ovary
41	chr19:39915400-39918800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:39915400-39918800	Weak transcription	Aorta	Aorta
43	chr19:39915400-39919000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr19:39915400-39921000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:39915400-39921200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr19:39915400-39921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:39915400-39921400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr19:39915400-39923000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:39915600-39918000	Weak transcription	Placenta	Placenta
50	chr19:39915600-39918200	Weak transcription	A549	lung

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