Variant report

Variant	rs4808198
Chromosome Location	chr19:19533630-19533631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19532975..19535791-chr19:19541066..19543559,2	MCF-7	breast:
2	chr19:19532624..19534313-chr19:19536405..19538480,2	MCF-7	breast:
3	chr19:19532571..19534201-chr19:19541059..19542925,2	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1000237	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10282	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10401193	0.85[ASN][1000 genomes]
rs10402308	0.84[ASN][1000 genomes]
rs10402451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10402627	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10404728	0.85[ASN][1000 genomes]
rs10405625	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408401	0.83[ASN][1000 genomes]
rs10410664	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414830	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419912	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422819	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047361	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054284	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1054930	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1063966	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669516	0.90[ASN][1000 genomes]
rs12972397	0.90[ASN][1000 genomes]
rs12973258	0.80[ASN][1000 genomes]
rs12975119	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12977524	0.90[ASN][1000 genomes]
rs1465695	0.85[ASN][1000 genomes]
rs1469712	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469713	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17288409	0.82[ASN][1000 genomes]
rs1808653	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858999	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865034	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2082421	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2099333	0.85[ASN][1000 genomes]
rs2099334	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163804	0.90[ASN][1000 genomes]
rs2163805	0.90[ASN][1000 genomes]
rs2288852	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304098	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2315279	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2315281	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2315610	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28478453	0.88[ASN][1000 genomes]
rs2905424	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2905425	0.81[EUR][1000 genomes]
rs2905431	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2905432	0.84[EUR][1000 genomes]
rs2905435	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2916069	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916073	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916074	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916076	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965175	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2965180	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965182	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965183	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965188	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2965189	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965198	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2965199	0.81[EUR][1000 genomes]
rs34277109	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34538000	0.82[EUR][1000 genomes]
rs34647936	0.90[ASN][1000 genomes]
rs35418933	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3752151	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3794990	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794993	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808199	0.90[ASN][1000 genomes]
rs4808200	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808202	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808203	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808208	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808950	0.82[ASN][1000 genomes]
rs4808955	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808957	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808959	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808960	0.90[ASN][1000 genomes]
rs4808961	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808964	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808965	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808967	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60003758	0.90[ASN][1000 genomes]
rs60321073	0.82[ASN][1000 genomes]
rs6511036	0.88[ASN][1000 genomes]
rs6511038	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7245983	0.84[ASN][1000 genomes]
rs7250658	0.86[ASN][1000 genomes]
rs7250893	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252888	0.82[ASN][1000 genomes]
rs7253807	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7256149	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747050	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751856	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751858	0.94[ASN][1000 genomes]
rs754255	0.90[ASN][1000 genomes]
rs892021	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892022	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9917108	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4808198	HAPLN4	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19518600-19549800	Weak transcription	Fetal Brain Female	brain
2	chr19:19520800-19546800	Weak transcription	Hela-S3	cervix
3	chr19:19521000-19545400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19521800-19536200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:19521800-19537600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:19522000-19545000	Weak transcription	Fetal Lung	lung
7	chr19:19522200-19534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:19522600-19537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:19525400-19538200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:19526400-19535000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:19527000-19534400	Enhancers	Fetal Muscle Trunk	muscle
14	chr19:19527000-19535600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr19:19528800-19539000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:19528800-19544200	Weak transcription	Fetal Heart	heart
17	chr19:19529000-19537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19529000-19539000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:19529200-19537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:19530000-19539000	Weak transcription	Placenta	Placenta
21	chr19:19530000-19539000	Weak transcription	NHLF	lung
22	chr19:19530000-19545400	Weak transcription	Colonic Mucosa	Colon
23	chr19:19530200-19533800	Weak transcription	Osteobl	bone
24	chr19:19530200-19537000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:19530200-19537800	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:19530200-19543400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr19:19530200-19547400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:19530400-19536800	Strong transcription	Fetal Intestine Small	intestine
29	chr19:19531200-19538000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr19:19531400-19534800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr19:19531400-19541600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:19531400-19545000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:19531600-19534800	Enhancers	Pancreas	Pancrea
34	chr19:19531600-19535600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:19531600-19535600	Enhancers	Lung	lung
36	chr19:19531600-19537400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr19:19531800-19534800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:19531800-19535400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:19531800-19538000	Enhancers	Liver	Liver
40	chr19:19532000-19534600	Strong transcription	Thymus	Thymus
41	chr19:19532000-19536600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:19532000-19538000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:19532200-19533800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:19532200-19533800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:19532200-19534000	Weak transcription	Fetal Intestine Large	intestine
46	chr19:19532200-19536000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:19532200-19536200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:19532200-19538000	Weak transcription	Dnd41	blood
49	chr19:19532200-19539400	Weak transcription	Stomach Mucosa	stomach
50	chr19:19532200-19541400	Weak transcription	Small Intestine	intestine

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