Variant report

Variant	rs6499544
Chromosome Location	chr16:71884021-71884022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71841492..71844076-chr16:71882492..71884911,2	MCF-7	breast:
2	chr16:71840076..71845074-chr16:71882668..71886861,6	K562	blood:
3	chr16:71883597..71885212-chr16:71917738..71919804,2	MCF-7	breast:
4	chr16:71883276..71884915-chr16:71893222..71894749,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11075896	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs11075897	0.82[YRI][hapmap]
rs13334187	1.00[ASW][hapmap];0.94[MKK][hapmap]
rs13334255	0.89[YRI][hapmap]
rs13334617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13335391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13337119	1.00[AMR][1000 genomes]
rs28431030	1.00[AFR][1000 genomes]
rs28436203	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs28450081	1.00[AMR][1000 genomes]
rs28450346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28523974	0.92[AFR][1000 genomes]
rs28711364	1.00[AMR][1000 genomes]
rs35999277	0.80[AFR][1000 genomes]
rs59358880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6499549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7186536	1.00[AMR][1000 genomes]
rs7191105	1.00[AMR][1000 genomes]
rs7198387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs7202000	1.00[AMR][1000 genomes]
rs73578375	1.00[AMR][1000 genomes]
rs73582271	1.00[AMR][1000 genomes]
rs73582274	1.00[AMR][1000 genomes]
rs73582278	1.00[AMR][1000 genomes]
rs73582282	1.00[AMR][1000 genomes]
rs73582529	1.00[AMR][1000 genomes]
rs73584107	1.00[AMR][1000 genomes]
rs73590035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73590039	0.89[AFR][1000 genomes]
rs73590051	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74027713	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045394	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs8048947	1.00[AMR][1000 genomes]
rs8051461	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059131	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs9302628	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs9673858	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921383	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9923154	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9923213	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9925225	1.00[AMR][1000 genomes]
rs9928298	1.00[ASW][hapmap];0.84[YRI][hapmap]
rs9928365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs9930588	0.84[YRI][hapmap]
rs9932715	1.00[AMR][1000 genomes]
rs9932742	0.95[LWK][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs9933862	1.00[AMR][1000 genomes]
rs9937049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9937974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941356	0.80[AFR][1000 genomes];1.00[AMR][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	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
3	nsv978166	chr16:71882680-71886018	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6499544	MARVELD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71881000-71902200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71881200-71889400	Weak transcription	Psoas Muscle	Psoas
3	chr16:71881200-71916600	Weak transcription	Small Intestine	intestine
4	chr16:71881600-71885600	Weak transcription	Fetal Brain Male	brain
5	chr16:71881600-71887200	Weak transcription	Fetal Heart	heart
6	chr16:71881800-71884800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:71881800-71885000	Strong transcription	Adipose Nuclei	Adipose
8	chr16:71881800-71885200	Strong transcription	NHDF-Ad	bronchial
9	chr16:71881800-71885400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:71881800-71886000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr16:71881800-71886000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr16:71881800-71886600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr16:71881800-71886600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:71881800-71887000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr16:71881800-71887200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr16:71881800-71887200	Strong transcription	Primary T cells from cord blood	blood
17	chr16:71881800-71887200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:71881800-71887400	Strong transcription	Fetal Intestine Large	intestine
19	chr16:71881800-71887800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr16:71881800-71887800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:71881800-71888000	Strong transcription	NHEK	skin
22	chr16:71881800-71889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr16:71881800-71890000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr16:71881800-71890200	Strong transcription	Placenta	Placenta
25	chr16:71881800-71890200	Strong transcription	Osteobl	bone
26	chr16:71881800-71890400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:71881800-71890800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr16:71881800-71890800	Strong transcription	Fetal Muscle Leg	muscle
29	chr16:71881800-71895800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:71881800-71897000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr16:71881800-71899000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr16:71881800-71902000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:71881800-71904600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:71881800-71914400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr16:71881800-71914600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:71882000-71884200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr16:71882000-71884400	Strong transcription	Thymus	Thymus
38	chr16:71882000-71884600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr16:71882000-71884600	Strong transcription	Fetal Kidney	kidney
40	chr16:71882000-71884600	Strong transcription	Stomach Mucosa	stomach
41	chr16:71882000-71884600	Strong transcription	K562	blood
42	chr16:71882000-71884800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:71882000-71884800	Strong transcription	Dnd41	blood
44	chr16:71882000-71885200	Strong transcription	HSMM	muscle
45	chr16:71882000-71885400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr16:71882000-71885600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:71882000-71885600	Strong transcription	Fetal Brain Female	brain
48	chr16:71882000-71885800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr16:71882000-71886000	Strong transcription	Colonic Mucosa	Colon
50	chr16:71882000-71887000	Strong transcription	Rectal Mucosa Donor 29	rectum

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