Variant report

Variant	rs2905425
Chromosome Location	chr19:19475717-19475718
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19475560..19479223-chr19:19494515..19497733,3	K562	blood:
2	chr19:19469546..19472054-chr19:19474284..19475951,2	MCF-7	breast:
3	chr19:19475375..19475969-chr19:19600833..19601839,3	K562	blood:
4	chr19:19475560..19478131-chr19:19494515..19496869,2	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1000237	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs1009136	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1010207	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10282	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10401193	0.80[JPT][hapmap]
rs10403731	0.82[ASN][1000 genomes]
rs10407952	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10409234	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10414830	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10418051	0.85[ASN][1000 genomes]
rs10419245	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10419672	0.93[ASN][1000 genomes]
rs10419912	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10421505	0.91[ASN][1000 genomes]
rs10422819	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs1054284	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs1063966	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs11085259	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11085261	0.82[ASN][1000 genomes]
rs12460764	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972397	0.81[JPT][hapmap]
rs12973258	0.80[JPT][hapmap]
rs12977524	0.80[JPT][hapmap]
rs12977937	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12982276	0.91[ASN][1000 genomes]
rs12985655	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469712	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1469713	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs15622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858999	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1859287	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2017964	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2023882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2023883	0.95[JPT][hapmap]
rs2074088	0.82[EUR][1000 genomes]
rs2074089	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074090	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074091	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074296	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs2074299	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074301	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2074303	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074550	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2163804	0.80[JPT][hapmap]
rs2269873	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285627	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2285628	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2285859	0.81[ASN][1000 genomes]
rs2288852	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2301668	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301669	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301671	0.82[ASN][1000 genomes]
rs2301784	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2301786	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304098	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs2315022	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2315025	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2315279	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2315281	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2315283	0.82[EUR][1000 genomes]
rs2315610	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2905421	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2905423	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2905424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905430	0.81[EUR][1000 genomes]
rs2905431	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905432	0.86[EUR][1000 genomes]
rs2916069	0.82[EUR][1000 genomes]
rs2916074	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs2916076	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs2965175	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965180	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs2965183	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs2965185	0.84[CEU][hapmap]
rs2965188	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2965189	0.92[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2965191	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2965193	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2965198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965199	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965200	0.87[EUR][1000 genomes]
rs34277109	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs34538000	0.87[EUR][1000 genomes]
rs35418933	0.90[EUR][1000 genomes]
rs3752151	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs3764567	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs3794990	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs3794993	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs3934667	0.80[AMR][1000 genomes]
rs4808193	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4808196	0.87[ASN][1000 genomes]
rs4808198	0.81[EUR][1000 genomes]
rs4808199	0.80[JPT][hapmap]
rs4808200	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4808203	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4808208	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4808937	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808938	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808939	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4808940	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4808941	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808942	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808957	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs4808959	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs4808960	0.81[JPT][hapmap]
rs4808961	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs4808964	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs4808965	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4808967	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs62135552	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511026	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511028	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511030	0.84[EUR][1000 genomes]
rs6511032	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511036	0.81[JPT][hapmap]
rs67720221	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6909	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs7245983	0.96[CEU][hapmap]
rs7246748	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7247309	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7250368	0.81[ASN][1000 genomes]
rs7252888	0.80[JPT][hapmap]
rs7254230	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254748	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7254927	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258508	0.90[ASN][1000 genomes]
rs7259434	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs735273	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs747050	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs757000	0.81[ASN][1000 genomes]
rs769267	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8101499	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8101938	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8103496	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105094	0.90[JPT][hapmap]
rs8105984	0.89[JPT][hapmap]
rs8108647	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs892021	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs892022	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs9304960	0.82[ASN][1000 genomes]
rs968525	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2905425	HAPLN4	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
2	chr19:19465200-19483600	Weak transcription	NH-A	brain
3	chr19:19467200-19477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:19468200-19477600	Weak transcription	Brain Substantia Nigra	brain
5	chr19:19468400-19476000	Weak transcription	Left Ventricle	heart
6	chr19:19468400-19477600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:19468400-19478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:19468600-19477600	Weak transcription	Fetal Lung	lung
9	chr19:19469200-19477600	Weak transcription	Brain Angular Gyrus	brain
10	chr19:19469400-19475800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:19469400-19482000	Weak transcription	Esophagus	oesophagus
12	chr19:19469800-19476000	Weak transcription	Brain Anterior Caudate	brain
13	chr19:19469800-19477400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:19469800-19477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:19469800-19477600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:19469800-19488400	Weak transcription	Gastric	stomach
17	chr19:19470000-19477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:19470000-19477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:19470400-19477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:19472200-19477600	Weak transcription	Brain Hippocampus Middle	brain
21	chr19:19472400-19475800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:19475200-19476000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:19475200-19476000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr19:19475200-19476200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr19:19475200-19476200	Enhancers	Primary hematopoietic stem cells	blood
26	chr19:19475200-19476200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19475200-19476200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr19:19475200-19476200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:19475200-19476200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr19:19475200-19476400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr19:19475200-19476400	Enhancers	Pancreas	Pancrea
32	chr19:19475200-19476400	Flanking Active TSS	Dnd41	blood
33	chr19:19475400-19475800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr19:19475400-19475800	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr19:19475400-19475800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr19:19475400-19475800	Flanking Active TSS	Colonic Mucosa	Colon
37	chr19:19475400-19475800	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr19:19475400-19475800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr19:19475400-19475800	Enhancers	Small Intestine	intestine
40	chr19:19475400-19475800	Flanking Active TSS	Thymus	Thymus
41	chr19:19475400-19475800	Weak transcription	Spleen	Spleen
42	chr19:19475400-19476000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr19:19475400-19476000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:19475400-19476000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr19:19475400-19476000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr19:19475400-19476000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr19:19475400-19476000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr19:19475400-19476000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:19475400-19476000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19475400-19476000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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