Variant report

Variant	rs2542176
Chromosome Location	chr18:12728657-12728658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12727153..12728721-chr18:12742306..12744471,2	K562	blood:
2	chr18:12726304..12729223-chr18:12948825..12951791,2	K562	blood:
3	chr18:12727418..12729485-chr18:12735947..12737729,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11080593	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11663219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11663260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539813	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs16939680	0.93[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs1833326	0.84[ASN][1000 genomes]
rs1893212	0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1893213	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1893214	0.81[ASN][1000 genomes]
rs2015197	0.87[ASN][1000 genomes]
rs2249830	0.93[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2542172	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2542174	0.93[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2542175	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542177	0.91[ASN][1000 genomes]
rs2847246	0.86[ASN][1000 genomes]
rs2847247	0.84[ASN][1000 genomes]
rs2847254	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847272	0.87[ASN][1000 genomes]
rs2847305	0.84[ASN][1000 genomes]
rs4796966	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4797698	0.81[ASN][1000 genomes]
rs4797701	0.86[ASN][1000 genomes]
rs507868	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs62095972	0.82[ASN][1000 genomes]
rs8086774	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs8089003	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
9	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv909405	chr18:12727224-12750499	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv909406	chr18:12727224-12761498	ZNF genes & repeats Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1062149	chr18:12728115-12783898	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2542176	SPIRE1	cis	parietal	SCAN
rs2542176	C22orf33	trans	cerebellum	SCAN
rs2542176	TUBB6	cis	cerebellum	SCAN
rs2542176	RALBP1	cis	cerebellum	SCAN
rs2542176	SPIRE1	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12714600-12728800	Weak transcription	Esophagus	oesophagus
2	chr18:12723000-12748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr18:12724200-12730000	Weak transcription	K562	blood
4	chr18:12724600-12729600	Weak transcription	Fetal Brain Female	brain
5	chr18:12724600-12729800	Weak transcription	HSMMtube	muscle
6	chr18:12725200-12729600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr18:12725200-12730200	Weak transcription	A549	lung
8	chr18:12725400-12729000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr18:12725600-12729400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr18:12725600-12729400	Weak transcription	HepG2	liver
11	chr18:12725800-12729800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr18:12725800-12729800	Weak transcription	Hela-S3	cervix
13	chr18:12726000-12728800	Weak transcription	NH-A	brain
14	chr18:12726200-12729400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr18:12726200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr18:12726600-12735600	Weak transcription	Right Atrium	heart
17	chr18:12726800-12730200	Weak transcription	HMEC	breast
18	chr18:12727000-12728800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr18:12727000-12728800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr18:12727000-12728800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr18:12727000-12728800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:12727000-12729400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr18:12727000-12729400	Weak transcription	GM12878-XiMat	blood
24	chr18:12727000-12730000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr18:12727000-12730200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr18:12727000-12730400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr18:12727000-12730600	Weak transcription	Placenta	Placenta
28	chr18:12727000-12745800	Weak transcription	Thymus	Thymus
29	chr18:12727200-12728800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:12727200-12728800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr18:12727200-12728800	Weak transcription	Primary B cells from cord blood	blood
32	chr18:12727200-12728800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr18:12727200-12728800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr18:12727200-12728800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr18:12727200-12728800	Weak transcription	Adipose Nuclei	Adipose
36	chr18:12727200-12728800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr18:12727200-12728800	Weak transcription	Fetal Lung	lung
38	chr18:12727200-12728800	Weak transcription	Left Ventricle	heart
39	chr18:12727200-12728800	Weak transcription	Lung	lung
40	chr18:12727200-12728800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr18:12727200-12728800	Weak transcription	Right Ventricle	heart
42	chr18:12727200-12728800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr18:12727200-12728800	Weak transcription	Spleen	Spleen
44	chr18:12727200-12729000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:12727200-12729000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr18:12727200-12729000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr18:12727200-12729000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr18:12727200-12729000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr18:12727200-12729000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:12727200-12729000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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