Variant report

Variant	rs12976025
Chromosome Location	chr19:19429220-19429221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19409469..19413871-chr19:19428728..19432308,7	K562	blood:
2	chr19:19428553..19432587-chr19:19515649..19520173,6	K562	blood:
3	chr19:19423866..19426693-chr19:19428690..19430948,2	MCF-7	breast:
4	chr19:19413265..19416143-chr19:19426604..19429701,3	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1009136	0.86[ASN][1000 genomes]
rs1010207	0.89[ASN][1000 genomes]
rs10402661	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403731	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10407952	0.89[ASN][1000 genomes]
rs10409234	0.87[ASN][1000 genomes]
rs10418051	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419245	0.86[ASN][1000 genomes]
rs10419672	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10421505	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10426780	0.83[ASN][1000 genomes]
rs11085259	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085261	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666553	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459676	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460764	0.87[ASN][1000 genomes]
rs12977937	0.87[ASN][1000 genomes]
rs12979148	0.81[AFR][1000 genomes]
rs12981974	0.83[EUR][1000 genomes]
rs12982276	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983137	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12985655	0.82[ASN][1000 genomes]
rs13964	0.81[ASN][1000 genomes]
rs15622	0.81[ASN][1000 genomes]
rs1859287	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017964	0.86[ASN][1000 genomes]
rs2023882	0.89[ASN][1000 genomes]
rs2023883	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074089	0.88[ASN][1000 genomes]
rs2074090	0.82[ASN][1000 genomes]
rs2074091	0.82[ASN][1000 genomes]
rs2074296	0.83[ASN][1000 genomes]
rs2074298	0.83[ASN][1000 genomes]
rs2074299	0.86[ASN][1000 genomes]
rs2074300	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074301	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074303	0.86[ASN][1000 genomes]
rs2074550	0.86[ASN][1000 genomes]
rs2074551	0.81[ASN][1000 genomes]
rs2269873	0.87[ASN][1000 genomes]
rs2285627	0.89[ASN][1000 genomes]
rs2285628	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285859	0.89[ASN][1000 genomes]
rs2301668	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301669	0.82[ASN][1000 genomes]
rs2301671	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301784	0.86[ASN][1000 genomes]
rs2301786	0.89[ASN][1000 genomes]
rs2315022	0.89[ASN][1000 genomes]
rs2315025	0.89[ASN][1000 genomes]
rs2905423	0.81[ASN][1000 genomes]
rs2965191	0.82[ASN][1000 genomes]
rs2965193	0.82[ASN][1000 genomes]
rs4808193	0.83[ASN][1000 genomes]
rs4808194	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808196	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4808937	0.89[ASN][1000 genomes]
rs4808938	0.89[ASN][1000 genomes]
rs4808939	0.94[ASN][1000 genomes]
rs4808940	0.85[ASN][1000 genomes]
rs4808941	0.85[ASN][1000 genomes]
rs4808942	0.90[ASN][1000 genomes]
rs62135552	0.86[ASN][1000 genomes]
rs6511026	0.86[ASN][1000 genomes]
rs6511028	0.89[ASN][1000 genomes]
rs67720221	0.92[ASN][1000 genomes]
rs7246748	0.86[ASN][1000 genomes]
rs7247309	0.86[ASN][1000 genomes]
rs7250368	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254230	0.87[ASN][1000 genomes]
rs7254748	0.87[ASN][1000 genomes]
rs7254927	0.89[ASN][1000 genomes]
rs7258508	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7259434	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735273	0.84[ASN][1000 genomes]
rs757000	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs769267	0.82[ASN][1000 genomes]
rs8101938	0.86[ASN][1000 genomes]
rs8103197	0.82[ASN][1000 genomes]
rs8103496	0.86[ASN][1000 genomes]
rs8105094	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8105984	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8108647	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304960	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs968525	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19384400-19430600	Weak transcription	Right Atrium	heart
2	chr19:19390800-19430000	Weak transcription	Psoas Muscle	Psoas
3	chr19:19416200-19430000	Weak transcription	Fetal Brain Male	brain
4	chr19:19419400-19429400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:19419600-19429600	Weak transcription	Hela-S3	cervix
6	chr19:19419600-19430200	Weak transcription	NH-A	brain
7	chr19:19421400-19429400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:19421400-19430200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:19421400-19430200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:19421600-19429400	Weak transcription	Stomach Mucosa	stomach
11	chr19:19421600-19430000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:19421600-19430000	Weak transcription	A549	lung
13	chr19:19421600-19430000	Weak transcription	HMEC	breast
14	chr19:19421600-19430000	Weak transcription	HSMMtube	muscle
15	chr19:19421600-19430200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:19421800-19429600	Weak transcription	Small Intestine	intestine
17	chr19:19421800-19430200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19423400-19429400	Weak transcription	GM12878-XiMat	blood
19	chr19:19424200-19430000	Weak transcription	Fetal Kidney	kidney
20	chr19:19425600-19430000	Weak transcription	HSMM	muscle
21	chr19:19426600-19430200	Weak transcription	NHDF-Ad	bronchial
22	chr19:19427200-19429800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:19427200-19430000	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:19427200-19430000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:19427200-19430200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:19427200-19430200	Weak transcription	Esophagus	oesophagus
27	chr19:19427400-19429400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:19427400-19429400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:19427400-19429400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19427400-19429400	Weak transcription	Liver	Liver
31	chr19:19427400-19429400	Weak transcription	Brain Anterior Caudate	brain
32	chr19:19427400-19429400	Weak transcription	Brain Substantia Nigra	brain
33	chr19:19427400-19429600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:19427400-19429600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:19427400-19429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:19427400-19429600	Weak transcription	Lung	lung
37	chr19:19427400-19429600	Weak transcription	Right Ventricle	heart
38	chr19:19427400-19429800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:19427400-19429800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:19427400-19429800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:19427400-19429800	Weak transcription	Fetal Lung	lung
42	chr19:19427400-19429800	Weak transcription	Pancreas	Pancrea
43	chr19:19427400-19429800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:19427400-19430000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:19427400-19430000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:19427400-19430000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:19427400-19430000	Weak transcription	Adipose Nuclei	Adipose
48	chr19:19427400-19430000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:19427400-19430000	Weak transcription	Colonic Mucosa	Colon
50	chr19:19427400-19430000	Weak transcription	Left Ventricle	heart

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