Variant report

Variant	rs12979565
Chromosome Location	chr19:19150183-19150184
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19143762..19145287-chr19:19149753..19152112,2	K562	blood:
2	chr19:19147736..19150233-chr19:19170434..19173422,2	K562	blood:
3	chr19:19148470..19151421-chr19:19152094..19154668,2	K562	blood:
4	chr19:19142730..19148953-chr19:19149447..19156213,13	K562	blood:
5	chr19:19148387..19150920-chr19:19203551..19206895,3	K562	blood:
6	chr19:19146038..19148163-chr19:19149447..19151209,2	K562	blood:
7	chr19:19148010..19150242-chr19:19312371..19314078,2	K562	blood:
8	chr19:19133809..19135508-chr19:19148686..19150405,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000064607	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000184162	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1007483	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10221504	0.94[ASN][1000 genomes]
rs10403222	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10403322	0.85[EUR][1000 genomes]
rs10404627	0.94[ASN][1000 genomes]
rs10405189	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10409164	0.94[ASN][1000 genomes]
rs10410451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10410568	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414676	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10422335	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10422906	0.94[ASN][1000 genomes]
rs10423742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10423815	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079543	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10854005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1124921	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666120	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11670204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670239	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11878368	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12016	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975676	0.94[ASN][1000 genomes]
rs12975754	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12976302	0.91[ASN][1000 genomes]
rs12978822	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12985799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1859267	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2107263	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158320	0.98[ASN][1000 genomes]
rs2240094	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240095	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2269869	0.84[CEU][hapmap]
rs2285851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2313736	0.95[ASN][1000 genomes]
rs2872394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3180770	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808172	0.90[CEU][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs4808179	0.98[ASN][1000 genomes]
rs4808184	0.94[ASN][1000 genomes]
rs4808902	0.95[ASN][1000 genomes]
rs4808904	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808905	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808906	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808911	0.98[ASN][1000 genomes]
rs4808913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808916	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6511010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511011	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511014	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511015	0.98[ASN][1000 genomes]
rs6511017	0.98[ASN][1000 genomes]
rs6511018	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6511021	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs7248399	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7248771	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250131	0.94[ASN][1000 genomes]
rs7253244	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255937	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7257635	0.90[ASN][1000 genomes]
rs7258637	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259510	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs757220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8101529	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103431	0.94[ASN][1000 genomes]
rs8104754	0.82[EUR][1000 genomes]
rs8104799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106146	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107710	0.88[ASN][1000 genomes]
rs8109654	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111634	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111635	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112566	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs916898	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304959	0.98[ASN][1000 genomes]
rs9676917	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12979565	TMEM161A	cis	Muscle Skeletal	GTEx
rs12979565	MED26	cis	cerebellum	SCAN
rs12979565	ZNF506	cis	parietal	SCAN
rs12979565	NDUFA13	cis	parietal	SCAN
rs12979565	KIAA1683	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19145000-19154800	Weak transcription	Aorta	Aorta
2	chr19:19145000-19174000	Weak transcription	Small Intestine	intestine
3	chr19:19145200-19153600	Weak transcription	Ovary	ovary
4	chr19:19145400-19153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:19145400-19165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:19145400-19171800	Weak transcription	Right Atrium	heart
7	chr19:19145600-19150200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:19145600-19150200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:19145600-19150200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:19145600-19150600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:19145600-19151000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:19145600-19151400	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:19145600-19151400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:19145600-19151600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:19145600-19153200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:19145600-19153400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:19145600-19153400	Weak transcription	Brain Substantia Nigra	brain
18	chr19:19145600-19153400	Weak transcription	Colonic Mucosa	Colon
19	chr19:19145600-19153400	Weak transcription	Gastric	stomach
20	chr19:19145600-19153400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:19145600-19153600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:19145600-19153600	Weak transcription	Brain Anterior Caudate	brain
23	chr19:19145600-19153600	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:19145600-19153600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:19145600-19153600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:19145600-19153800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:19145600-19154000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:19145600-19154600	Weak transcription	HUVEC	blood vessel
29	chr19:19145600-19154600	Weak transcription	NHDF-Ad	bronchial
30	chr19:19145600-19154800	Weak transcription	Brain Angular Gyrus	brain
31	chr19:19145600-19154800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:19145600-19159600	Weak transcription	NH-A	brain
33	chr19:19145600-19172200	Weak transcription	Stomach Mucosa	stomach
34	chr19:19145600-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:19145600-19173800	Weak transcription	Fetal Kidney	kidney
36	chr19:19145800-19150200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:19145800-19150200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:19145800-19153400	Weak transcription	Spleen	Spleen
39	chr19:19146200-19150200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:19146200-19150400	Strong transcription	Fetal Stomach	stomach
41	chr19:19146200-19151600	Weak transcription	Adipose Nuclei	Adipose
42	chr19:19146200-19153600	Weak transcription	Right Ventricle	heart
43	chr19:19146200-19154000	Weak transcription	Left Ventricle	heart
44	chr19:19146400-19150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:19146400-19150200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:19146400-19150400	Weak transcription	Fetal Brain Male	brain
47	chr19:19146400-19150400	Weak transcription	HepG2	liver
48	chr19:19146400-19150600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19146400-19151000	Weak transcription	Pancreas	Pancrea
50	chr19:19146400-19151400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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