Variant report

Variant	rs1546
Chromosome Location	chr11:9514361-9514362
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	chr11:9510455..9512586-chr11:9513778..9516603,2	K562	blood:
2	chr11:9481348..9484477-chr11:9512736..9516617,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM41B-3	chr11:9514086-9514557	ENSG00000255180.1

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082685	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10840246	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11042318	0.80[CEU][hapmap]
rs11042365	0.84[EUR][1000 genomes]
rs11042367	0.84[EUR][1000 genomes]
rs11042379	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042401	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042402	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11600094	0.86[AMR][1000 genomes]
rs11600357	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11602025	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11602056	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11607631	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274646	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12274655	0.86[AMR][1000 genomes]
rs12279202	1.00[CEU][hapmap]
rs12280032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280819	0.92[AMR][1000 genomes]
rs12284187	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12284407	0.86[AMR][1000 genomes]
rs12285570	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12292907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12293264	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12293634	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12293911	0.87[EUR][1000 genomes]
rs12419780	0.86[AMR][1000 genomes]
rs16906804	1.00[CEU][hapmap]
rs36048375	1.00[CEU][hapmap]
rs4910052	1.00[CEU][hapmap]
rs4910054	0.81[AMR][1000 genomes]
rs4910466	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910467	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910469	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4910471	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910475	0.86[AMR][1000 genomes]
rs56116319	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56320702	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9988896	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv7670	chr11:9500895-9514750	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1546	ZNF143	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9483600-9518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:9485200-9520000	Weak transcription	Stomach Mucosa	stomach
4	chr11:9489600-9524000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:9489800-9523400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:9491400-9525400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:9492000-9527200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:9492200-9525400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:9492800-9527800	Strong transcription	Fetal Stomach	stomach
11	chr11:9495600-9525400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:9496200-9520000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:9496200-9522600	Weak transcription	Fetal Heart	heart
14	chr11:9496600-9516000	Weak transcription	Fetal Brain Male	brain
15	chr11:9496600-9517000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:9496600-9528200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:9497400-9517400	Weak transcription	Small Intestine	intestine
18	chr11:9499200-9526000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:9500200-9516000	Weak transcription	Pancreas	Pancrea
20	chr11:9500400-9522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:9500600-9519800	Weak transcription	A549	lung
22	chr11:9501400-9522600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:9501600-9517400	Weak transcription	Esophagus	oesophagus
24	chr11:9501600-9519800	Weak transcription	Fetal Kidney	kidney
25	chr11:9501800-9515800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:9501800-9516000	Weak transcription	Brain Angular Gyrus	brain
27	chr11:9501800-9516000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:9501800-9517200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:9501800-9517200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:9501800-9534000	Weak transcription	Psoas Muscle	Psoas
31	chr11:9502200-9516000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:9502800-9517200	Weak transcription	Colonic Mucosa	Colon
33	chr11:9503000-9515600	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:9503000-9516400	Weak transcription	Brain Substantia Nigra	brain
35	chr11:9503000-9517200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:9503000-9519600	Weak transcription	Gastric	stomach
37	chr11:9503000-9521000	Weak transcription	Aorta	Aorta
38	chr11:9505200-9525200	Strong transcription	Placenta	Placenta
39	chr11:9506000-9525200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr11:9506800-9517400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:9506800-9525400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:9506800-9525400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:9507000-9523400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr11:9507200-9523400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:9507200-9525400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:9507200-9525400	Strong transcription	Adipose Nuclei	Adipose
47	chr11:9507800-9515600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:9507800-9515600	Weak transcription	K562	blood
49	chr11:9508800-9525000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:9509200-9523600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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