Variant report

Variant	rs6506899
Chromosome Location	chr18:28805802-28805803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28805153..28808185-chr18:28812239..28815732,4	K562	blood:

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10164077	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs10438930	0.82[CHB][hapmap]
rs11081691	1.00[CHB][hapmap]
rs1154850	0.82[CHB][hapmap];0.88[YRI][hapmap]
rs11659665	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11660638	0.81[EUR][1000 genomes]
rs11663622	0.82[CHB][hapmap]
rs11663676	0.82[CHB][hapmap]
rs11664596	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872734	0.82[CHB][hapmap]
rs11875510	0.82[CHB][hapmap]
rs11875560	0.82[CHB][hapmap]
rs12606446	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12606722	0.82[EUR][1000 genomes]
rs12607370	1.00[CHB][hapmap]
rs12957659	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958069	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958073	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958351	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958377	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12959058	0.82[EUR][1000 genomes]
rs12962355	1.00[CHB][hapmap]
rs12963302	1.00[CHB][hapmap]
rs12964422	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964443	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964744	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964748	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964839	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964907	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965148	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965177	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965803	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965829	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966119	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12967407	1.00[CHB][hapmap]
rs12969200	1.00[CHB][hapmap]
rs1426309	1.00[CHB][hapmap]
rs1426310	1.00[CHB][hapmap]
rs1426311	1.00[CHB][hapmap]
rs1544880	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593511	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17658464	0.81[EUR][1000 genomes]
rs17715828	1.00[CHB][hapmap]
rs2007149	0.82[CHB][hapmap]
rs2042720	0.82[EUR][1000 genomes]
rs2114269	1.00[CHB][hapmap]
rs2162273	0.82[CHB][hapmap]
rs2162274	0.82[EUR][1000 genomes]
rs2199301	1.00[CHB][hapmap]
rs2219583	0.82[CHB][hapmap]
rs28372393	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510667	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28615832	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28633353	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901124	1.00[CHB][hapmap]
rs2901125	0.82[CHB][hapmap]
rs34187983	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212801	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34301793	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34530511	0.82[EUR][1000 genomes]
rs34634416	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664857	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743470	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136508	0.81[EUR][1000 genomes]
rs35220971	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35229932	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35257713	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35362621	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35596545	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909227	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810007	0.82[CHB][hapmap]
rs3810008	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs4349226	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356544	0.82[CHB][hapmap];0.87[YRI][hapmap]
rs4408611	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4517864	0.83[EUR][1000 genomes]
rs4539673	0.82[EUR][1000 genomes]
rs55776955	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308568	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087700	0.83[EUR][1000 genomes]
rs62087701	0.82[EUR][1000 genomes]
rs62087702	0.82[EUR][1000 genomes]
rs62087703	0.82[EUR][1000 genomes]
rs62090396	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62090401	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506903	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6506904	0.82[EUR][1000 genomes]
rs6506914	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs6506916	0.82[CHB][hapmap]
rs67014182	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226461	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7229569	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7230461	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7231460	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7232206	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7233743	0.82[CHB][hapmap];0.81[YRI][hapmap]
rs7234662	0.82[CHB][hapmap]
rs7234854	0.82[CHB][hapmap]
rs7235354	1.00[CHB][hapmap]
rs7235384	0.82[EUR][1000 genomes]
rs7235951	0.82[CHB][hapmap]
rs7235975	0.82[CHB][hapmap]
rs7236225	0.82[CHB][hapmap]
rs7237370	0.82[CHB][hapmap]
rs7237383	0.82[CHB][hapmap]
rs7237419	0.82[CHB][hapmap]
rs7239695	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240897	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7242742	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7243151	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243262	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243638	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243885	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243922	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243984	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244015	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244050	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244153	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244510	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245008	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72914749	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765054	0.82[CHB][hapmap]
rs8087103	0.82[EUR][1000 genomes]
rs8087410	0.82[CHB][hapmap]
rs8087786	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8088637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8088973	0.85[EUR][1000 genomes]
rs8089598	0.84[EUR][1000 genomes]
rs8089762	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8091151	0.82[CHB][hapmap]
rs8091579	0.82[CHB][hapmap]
rs8091715	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8091847	0.82[CHB][hapmap]
rs8091871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs966376	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9946611	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947444	0.82[CHB][hapmap]
rs9948210	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs9950209	0.82[CHB][hapmap]
rs9950622	1.00[CHB][hapmap]
rs9950769	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950949	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950971	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951016	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951341	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs9956026	0.82[CHB][hapmap]
rs9957758	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9963626	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28797400-28806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:28803800-28807000	Weak transcription	Right Ventricle	heart
3	chr18:28803800-28807200	Weak transcription	Left Ventricle	heart
4	chr18:28804800-28809600	Enhancers	GM12878-XiMat	blood
5	chr18:28805000-28808200	Enhancers	Fetal Heart	heart
6	chr18:28805000-28811000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:28805200-28806000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr18:28805200-28806000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:28805200-28806200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:28805200-28806200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr18:28805200-28806200	Enhancers	A549	lung
12	chr18:28805200-28806400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:28805200-28806400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:28805200-28806400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr18:28805200-28806400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr18:28805200-28806400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr18:28805200-28806400	Enhancers	NH-A	brain
18	chr18:28805200-28806600	Enhancers	Osteobl	bone
19	chr18:28805200-28807400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr18:28805400-28806000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr18:28805400-28806000	Enhancers	Hela-S3	cervix
22	chr18:28805400-28806000	Flanking Active TSS	HepG2	liver
23	chr18:28805400-28806200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr18:28805400-28806200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr18:28805400-28806200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr18:28805400-28807600	Active TSS	Right Atrium	heart
27	chr18:28805600-28806000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr18:28805600-28806000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr18:28805600-28806000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:28805600-28806000	Enhancers	Fetal Kidney	kidney
31	chr18:28805600-28806000	Enhancers	Placenta	Placenta
32	chr18:28805600-28806000	Enhancers	Gastric	stomach
33	chr18:28805600-28806200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr18:28805600-28806200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:28805600-28806200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr18:28805600-28806200	Enhancers	Pancreas	Pancrea
37	chr18:28805600-28806200	Enhancers	HMEC	breast
38	chr18:28805800-28806000	Enhancers	Liver	Liver
39	chr18:28805800-28806600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:28805800-28806600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr18:28805800-28806600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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