Variant report

Variant	rs17659896
Chromosome Location	chr18:12998655-12998656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12996489..12998450-chr18:12998497..13000010,2	K562	blood:
2	chr18:12988481..12994468-chr18:12998354..13003992,8	MCF-7	breast:
3	chr18:12995796..12999639-chr18:13011054..13013784,3	K562	blood:
4	chr18:12996926..12999710-chr18:13000576..13003531,2	K562	blood:

Variant related genes	Relation type
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10163827	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11080617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080618	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659979	0.82[CHB][hapmap]
rs11661559	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11661908	0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs11662634	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11662766	0.87[JPT][hapmap]
rs11664213	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12327306	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12604538	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12605267	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607398	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607919	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs12953783	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12957380	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960349	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961596	0.97[ASN][1000 genomes]
rs12963426	0.99[ASN][1000 genomes]
rs12967249	0.88[AMR][1000 genomes]
rs12970503	0.97[ASN][1000 genomes]
rs12970508	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs12971036	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs13381134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13381779	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523064	0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs17603207	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17659689	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17659749	0.95[ASN][1000 genomes]
rs2015763	0.85[ASN][1000 genomes]
rs2282540	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28551661	0.99[ASN][1000 genomes]
rs28654613	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34117444	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34166083	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34302481	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35368962	0.96[ASN][1000 genomes]
rs35563947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809914	0.88[ASN][1000 genomes]
rs3976787	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs496270	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56263236	0.82[ASN][1000 genomes]
rs6505772	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs68004799	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71353241	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7228684	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7229869	0.85[ASN][1000 genomes]
rs7230391	0.99[ASN][1000 genomes]
rs7230435	0.87[ASN][1000 genomes]
rs7234938	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236710	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7237711	0.84[ASN][1000 genomes]
rs7239486	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8083393	0.87[JPT][hapmap]
rs8083401	0.86[ASN][1000 genomes]
rs8086882	0.83[ASN][1000 genomes]
rs8089724	0.97[ASN][1000 genomes]
rs8090667	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs8093236	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs8093576	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8096860	0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs8566	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9950241	0.97[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	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
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17659896	CEP192	cis	Thyroid	GTEx
rs17659896	CEP192	cis	parietal	SCAN
rs17659896	CEP192	cis	Artery Tibial	GTEx
rs17659896	CEP192	cis	lung	GTEx
rs17659896	CEP192	cis	cerebellum	SCAN
rs17659896	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs17659896	CEP192	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992000-13000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:12992000-13004400	Weak transcription	Esophagus	oesophagus
3	chr18:12992200-13004800	Weak transcription	Aorta	Aorta
4	chr18:12992400-13000400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:12992400-13000600	Weak transcription	Placenta	Placenta
6	chr18:12992400-13004400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:12992600-13000400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:12992800-13004000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
11	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
13	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:12993000-13001400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr18:12993000-13006400	Weak transcription	Fetal Brain Female	brain
16	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr18:12993200-13000200	Weak transcription	HSMM	muscle
18	chr18:12993200-13000400	Weak transcription	Adipose Nuclei	Adipose
19	chr18:12993200-13001000	Weak transcription	Fetal Intestine Large	intestine
20	chr18:12993200-13001200	Weak transcription	A549	lung
21	chr18:12993200-13004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr18:12993200-13004800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr18:12993200-13006800	Weak transcription	HSMMtube	muscle
24	chr18:12993200-13007000	Weak transcription	Brain Substantia Nigra	brain
25	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:12993200-13008400	Weak transcription	Osteobl	bone
27	chr18:12993200-13008800	Weak transcription	NHLF	lung
28	chr18:12993400-12999400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr18:12993400-12999400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr18:12993400-12999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr18:12993400-13000200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr18:12993400-13000200	Weak transcription	Liver	Liver
33	chr18:12993400-13000200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr18:12993400-13000200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr18:12993400-13000600	Weak transcription	Fetal Stomach	stomach
36	chr18:12993400-13000800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:12993400-13003000	Weak transcription	Fetal Muscle Leg	muscle
38	chr18:12993400-13003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr18:12993400-13006200	Weak transcription	NH-A	brain
40	chr18:12993400-13006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr18:12993400-13008200	Weak transcription	Brain Angular Gyrus	brain
42	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
43	chr18:12993600-13000200	Weak transcription	Primary B cells from cord blood	blood
44	chr18:12993600-13000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr18:12993600-13000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr18:12993600-13000400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr18:12993600-13000400	Weak transcription	Lung	lung
48	chr18:12993600-13001800	Weak transcription	Brain Germinal Matrix	brain
49	chr18:12993600-13003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr18:12993600-13011800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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