Variant report

Variant	rs6499540
Chromosome Location	chr16:71822250-71822251
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71820240..71822383-chr16:71824559..71826827,2	K562	blood:
2	chr16:71821888..71825986-chr16:71827605..71831800,6	MCF-7	breast:
3	chr16:71820044..71826852-chr16:71835906..71843775,16	K562	blood:
4	chr16:71821041..71823920-chr16:71838306..71840822,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1058750	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10852502	1.00[ASN][1000 genomes]
rs10852503	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075894	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075901	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11075904	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075905	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11862723	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923990	0.81[EUR][1000 genomes]
rs12929547	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364210	1.00[ASN][1000 genomes]
rs1392484	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423983	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[ASN][1000 genomes]
rs2133773	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	1.00[ASN][1000 genomes]
rs2334877	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2334880	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	1.00[ASN][1000 genomes]
rs4788548	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4788550	0.84[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788553	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788557	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788559	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4788810	1.00[ASN][1000 genomes]
rs4788813	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4788820	1.00[ASN][1000 genomes]
rs4788822	1.00[ASN][1000 genomes]
rs4788823	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788828	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788830	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6499527	1.00[ASN][1000 genomes]
rs6499528	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6499529	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186112	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187948	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7190487	1.00[ASN][1000 genomes]
rs7193549	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7195059	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201712	0.85[EUR][1000 genomes]
rs7202479	1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204118	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7204608	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7204967	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044144	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8051968	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052910	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053186	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053745	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055419	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8062188	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302630	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9635524	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979790	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9888756	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929840	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs9929985	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930015	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9931074	1.00[ASN][1000 genomes]
rs9934301	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937511	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939458	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6499540	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs6499540	PHLPP2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:71793200-71830400	Weak transcription	Fetal Heart	heart
3	chr16:71797000-71823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:71803000-71823800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr16:71805000-71823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:71807800-71822600	Weak transcription	Aorta	Aorta
7	chr16:71808000-71829800	Weak transcription	NHLF	lung
8	chr16:71808400-71828800	Weak transcription	HSMMtube	muscle
9	chr16:71811800-71822400	Weak transcription	Gastric	stomach
10	chr16:71811800-71822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:71811800-71826600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:71812000-71822600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:71812000-71822800	Weak transcription	Spleen	Spleen
14	chr16:71812000-71823000	Weak transcription	Pancreas	Pancrea
15	chr16:71812400-71822400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr16:71812600-71822400	Weak transcription	Esophagus	oesophagus
17	chr16:71812600-71825800	Weak transcription	Right Atrium	heart
18	chr16:71815000-71823400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:71815200-71823400	Strong transcription	Placenta	Placenta
20	chr16:71815400-71823800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr16:71816000-71840400	Weak transcription	Fetal Kidney	kidney
22	chr16:71816200-71823400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:71816200-71823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:71816800-71823400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:71816800-71823400	Strong transcription	Liver	Liver
26	chr16:71817000-71822600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr16:71817800-71822600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr16:71817800-71823400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:71818000-71823400	Strong transcription	Fetal Thymus	thymus
30	chr16:71818000-71823600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:71818000-71823600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:71818200-71823200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:71818200-71823400	Strong transcription	Adipose Nuclei	Adipose
34	chr16:71818200-71823400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:71818200-71823600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr16:71818200-71823600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr16:71818200-71823600	Strong transcription	Fetal Muscle Leg	muscle
38	chr16:71818200-71823600	Strong transcription	HepG2	liver
39	chr16:71818400-71822600	Weak transcription	Stomach Mucosa	stomach
40	chr16:71818600-71823400	Strong transcription	Fetal Stomach	stomach
41	chr16:71819000-71823200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr16:71819000-71823600	Strong transcription	Fetal Intestine Large	intestine
43	chr16:71819200-71822800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr16:71819200-71823400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:71819200-71823400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr16:71819200-71823400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr16:71819200-71823600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr16:71819800-71823400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr16:71819800-71823400	Strong transcription	Fetal Lung	lung
50	chr16:71819800-71823400	Strong transcription	HSMM	muscle

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