Variant report

Variant	rs2902856
Chromosome Location	chr18:12984340-12984341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12946346..12949271-chr18:12983638..12986634,3	K562	blood:
2	chr18:12951983..12953642-chr18:12983977..12986674,2	K562	blood:
3	chr18:12977407..12979654-chr18:12980274..12984512,3	K562	blood:
4	chr18:12972698..12975600-chr18:12984314..12986199,2	MCF-7	breast:
5	chr18:12975871..12977998-chr18:12984226..12986742,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10221326	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10221384	0.83[EUR][1000 genomes]
rs11080620	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11663049	0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605638	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12954256	0.85[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12955780	1.00[ASW][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474043	1.00[ASW][hapmap];0.85[CEU][hapmap];0.80[GIH][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1786263	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786270	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1786279	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787000	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787003	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787004	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787008	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973779	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28619103	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28641764	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35790309	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3809912	1.00[ASW][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472702	0.82[EUR][1000 genomes]
rs472992	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs473580	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474337	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs475139	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs478006	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs478399	0.82[EUR][1000 genomes]
rs482360	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs482577	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs490853	0.94[AMR][1000 genomes]
rs491349	0.81[EUR][1000 genomes]
rs492723	0.83[EUR][1000 genomes]
rs498685	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4995995	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs518145	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527839	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs529620	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs547084	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs554719	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs554854	0.82[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs556371	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556536	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs557846	0.84[EUR][1000 genomes]
rs562151	0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565832	0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs567031	0.82[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs569453	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs570505	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs576963	0.94[CHD][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs578208	0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505775	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505776	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505777	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505780	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692833	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs692964	0.82[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71353243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7226616	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7229870	0.82[ASW][hapmap];0.81[CEU][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233600	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233814	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7234094	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234960	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236162	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7236764	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7237236	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7241536	0.81[JPT][hapmap]
rs7243660	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8088313	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089123	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8097038	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097125	0.83[CEU][hapmap];0.81[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783859	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783903	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9948139	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9948681	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9949589	0.82[CEU][hapmap];0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9949682	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9951698	0.86[AMR][1000 genomes]
rs9952698	0.83[EUR][1000 genomes]
rs9958369	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9961669	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9964466	1.00[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9965977	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2902856	CEP192	cis	Stomach	GTEx
rs2902856	CEP192	cis	Nerve Tibial	GTEx
rs2902856	CEP192	cis	Esophagus Mucosa	GTEx
rs2902856	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs2902856	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs2902856	CEP192	cis	Esophagus Muscularis	GTEx
rs2902856	CEP192	cis	Whole Blood	GTEx
rs2902856	CEP192	cis	multi-tissue	Pritchard
rs2902856	CEP192	cis	Artery Tibial	GTEx
rs2902856	CEP192	cis	Thyroid	GTEx
rs2902856	CEP192	cis	Artery Aorta	GTEx
rs2902856	CEP192	cis	Adipose Subcutaneous	GTEx
rs2902856	CEP192	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
3	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
4	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:12972800-12990000	Weak transcription	Brain Substantia Nigra	brain
8	chr18:12973200-12990200	Weak transcription	Small Intestine	intestine
9	chr18:12974200-12990200	Weak transcription	Brain Hippocampus Middle	brain
10	chr18:12975800-12990200	Weak transcription	Right Ventricle	heart
11	chr18:12976000-12990200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr18:12976400-12990000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr18:12976400-12990000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr18:12976400-12990000	Weak transcription	Colon Smooth Muscle	Colon
15	chr18:12976400-12990000	Weak transcription	Stomach Mucosa	stomach
16	chr18:12976400-12990200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12976400-12990200	Weak transcription	Brain Angular Gyrus	brain
18	chr18:12976400-12990200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr18:12976400-12990200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:12976400-12990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr18:12976600-12990000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr18:12976600-12990000	Weak transcription	Fetal Heart	heart
23	chr18:12976600-12990200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr18:12976600-12990200	Weak transcription	Brain Anterior Caudate	brain
25	chr18:12976600-12990200	Weak transcription	Esophagus	oesophagus
26	chr18:12976600-12990200	Weak transcription	Spleen	Spleen
27	chr18:12976600-12990400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr18:12976600-12990800	Weak transcription	Aorta	Aorta
29	chr18:12976800-12990200	Weak transcription	Fetal Lung	lung
30	chr18:12977400-12990600	Weak transcription	HSMMtube	muscle
31	chr18:12978000-12985000	Weak transcription	NHDF-Ad	bronchial
32	chr18:12978600-12989200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr18:12978600-12990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:12978600-12990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:12978600-12990200	Weak transcription	Pancreas	Pancrea
36	chr18:12978800-12986800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr18:12978800-12990000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:12978800-12990000	Weak transcription	NHLF	lung
39	chr18:12979000-12989400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12979000-12990000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr18:12979000-12990000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr18:12981400-12985600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:12981400-12986000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:12981400-12987200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr18:12981600-12987200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr18:12981600-12987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr18:12981600-12987800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12981800-12986200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr18:12982000-12985000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr18:12982000-12985200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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