Variant report

Variant	rs2847286
Chromosome Location	chr18:12817815-12817816
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	chr18:12817654..12819738-chr18:12836432..12839410,2	K562	blood:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11663472	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11876290	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12971201	0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs2542152	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2542157	1.00[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2542160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542162	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs2542167	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2847256	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2847257	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2847258	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2847261	0.81[ASN][1000 genomes]
rs2847276	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847277	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847281	0.84[CEU][hapmap];0.90[GIH][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs2847285	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847291	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2847292	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847299	0.90[ASN][1000 genomes]
rs2852151	0.81[CEU][hapmap];0.93[GIH][hapmap]
rs45456495	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478582	0.86[GIH][hapmap];0.88[YRI][hapmap]
rs4797709	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs674222	0.88[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs8087237	0.86[GIH][hapmap];0.88[YRI][hapmap]
rs888269	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs888271	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
8	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2847286	PTPN2	cis	parietal	SCAN
rs2847286	RP11-973H7.4	cis	Whole Blood	GTEx
rs2847286	MC5R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
3	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
4	chr18:12790200-12828000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr18:12790600-12820000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12791200-12819600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr18:12791400-12819600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
9	chr18:12791600-12828000	Weak transcription	HUVEC	blood vessel
10	chr18:12791800-12821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:12792800-12819600	Weak transcription	NHLF	lung
12	chr18:12797800-12819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:12806400-12827600	Strong transcription	Dnd41	blood
15	chr18:12806800-12827400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr18:12807200-12819600	Weak transcription	Brain Substantia Nigra	brain
17	chr18:12807200-12826600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
19	chr18:12807400-12821400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12808400-12818800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr18:12808400-12818800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr18:12808600-12827400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr18:12808800-12818400	Strong transcription	Primary T cells from cord blood	blood
24	chr18:12808800-12819000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr18:12808800-12827200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr18:12809000-12828000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr18:12809000-12828000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr18:12809400-12819600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:12809400-12819800	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:12809600-12824600	Weak transcription	Esophagus	oesophagus
31	chr18:12809600-12825200	Weak transcription	Aorta	Aorta
32	chr18:12809600-12828000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr18:12809600-12833200	Weak transcription	HSMM	muscle
34	chr18:12809600-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:12809600-12838200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr18:12810600-12818000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr18:12811000-12818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr18:12811200-12821800	Weak transcription	Stomach Mucosa	stomach
39	chr18:12811600-12818000	Strong transcription	Fetal Intestine Large	intestine
40	chr18:12811600-12819400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr18:12811600-12828000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr18:12811800-12827400	Weak transcription	Psoas Muscle	Psoas
43	chr18:12812000-12818800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:12812000-12819400	Strong transcription	Thymus	Thymus
45	chr18:12812000-12838400	Weak transcription	Right Ventricle	heart
46	chr18:12812200-12819000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:12812600-12819400	Strong transcription	Fetal Thymus	thymus
48	chr18:12812600-12822600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr18:12812800-12819800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr18:12813200-12818600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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