Variant report

Variant	rs11075896
Chromosome Location	chr16:71703252-71703253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71682067..71684821-chr16:71701301..71704672,3	MCF-7	breast:
2	chr16:71702434..71705433-chr8:9912003..9914488,2	K562	blood:
3	chr16:71696570..71698748-chr16:71701412..71704354,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175806	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11075897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331092	1.00[ASW][hapmap];0.88[LWK][hapmap]
rs13331951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334187	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	0.91[AFR][1000 genomes]
rs13337162	0.96[AFR][1000 genomes]
rs13337224	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338868	0.88[LWK][hapmap]
rs13339574	0.92[AFR][1000 genomes]
rs28436203	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28487278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681277	0.93[AFR][1000 genomes]
rs28712876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28744680	0.83[AFR][1000 genomes]
rs28757746	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56209933	0.83[AFR][1000 genomes]
rs57187537	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57827931	0.92[AFR][1000 genomes]
rs58324033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61258964	0.82[AFR][1000 genomes]
rs6499544	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs7191105	0.82[YRI][hapmap]
rs7196013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045394	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs8048170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059131	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063658	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302626	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9302628	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921383	1.00[ASW][hapmap];0.94[MKK][hapmap]
rs9921552	0.96[AFR][1000 genomes]
rs9923154	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9924829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924862	0.96[AFR][1000 genomes]
rs9925371	0.93[AFR][1000 genomes]
rs9925712	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926077	0.93[AFR][1000 genomes]
rs9927004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	1.00[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.96[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	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11075896	MARVELD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71671800-71704000	Weak transcription	Fetal Brain Male	brain
2	chr16:71672000-71741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:71674800-71704600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:71675000-71724000	Weak transcription	Esophagus	oesophagus
5	chr16:71681200-71710800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:71681200-71716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:71683800-71704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:71684000-71704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:71685200-71741200	Weak transcription	Psoas Muscle	Psoas
11	chr16:71685400-71718800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:71685800-71726000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr16:71686200-71705400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:71686800-71717200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr16:71687800-71725000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr16:71688600-71703400	Weak transcription	Pancreas	Pancrea
17	chr16:71688600-71704000	Weak transcription	Gastric	stomach
18	chr16:71689000-71710000	Weak transcription	Thymus	Thymus
19	chr16:71690600-71703400	Weak transcription	Right Ventricle	heart
20	chr16:71690600-71706400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr16:71690600-71708800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:71690600-71709600	Weak transcription	Small Intestine	intestine
23	chr16:71690600-71733600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr16:71690600-71741200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:71690800-71725600	Weak transcription	Fetal Thymus	thymus
26	chr16:71691200-71703800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:71692800-71703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:71693000-71704000	Weak transcription	Fetal Heart	heart
29	chr16:71693000-71756400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr16:71694400-71705600	Strong transcription	Fetal Stomach	stomach
31	chr16:71694600-71706600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:71694800-71710400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:71695000-71707400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:71695000-71710800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr16:71695000-71725200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:71695000-71726000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr16:71695200-71719200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:71695200-71724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr16:71695200-71725200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:71695600-71705400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr16:71696000-71706000	Strong transcription	Adipose Nuclei	Adipose
42	chr16:71696000-71719000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:71696200-71705400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:71696200-71706000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr16:71696200-71713400	Strong transcription	Brain Germinal Matrix	brain
46	chr16:71696400-71705400	Strong transcription	Osteobl	bone
47	chr16:71696400-71707600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr16:71696400-71720000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:71696400-71725200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr16:71696600-71705400	Strong transcription	Placenta	Placenta

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