Variant report

Variant	rs17741796
Chromosome Location	chr18:29409319-29409320
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	chr18:29407667..29410510-chr18:29494386..29496036,2	K562	blood:
2	chr18:29408804..29411024-chr18:29521543..29524021,2	K562	blood:

Variant related genes	Relation type
ENSG00000153339	Chromatin interaction
ENSG00000263823	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10468902	0.95[JPT][hapmap]
rs11081717	0.97[ASN][1000 genomes]
rs11081718	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs11081719	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11081720	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11081722	0.87[ASN][1000 genomes]
rs11081723	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081724	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081729	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11659244	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11660557	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11661525	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11662341	0.95[JPT][hapmap]
rs11662697	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11665424	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11877256	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12604691	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12605636	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12606354	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12606379	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12606882	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs12606962	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12607786	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608051	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17741967	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742014	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17742105	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17804129	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276144	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291239	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28654480	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34180462	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35275842	0.83[ASN][1000 genomes]
rs3737373	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737374	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs3810001	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3925536	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4539674	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4545895	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55706254	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56303347	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58098304	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614342	0.95[JPT][hapmap]
rs62093860	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62093864	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62093866	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62093867	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62093868	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62093869	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62093873	0.86[ASN][1000 genomes]
rs62093900	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62093901	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62093903	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62095507	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62095508	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62095509	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62095510	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62095543	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62095544	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62095545	0.85[ASN][1000 genomes]
rs62095546	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62095547	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62095548	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6506947	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7226615	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226713	0.86[ASN][1000 genomes]
rs7228817	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231114	0.95[JPT][hapmap]
rs7233234	0.88[ASN][1000 genomes]
rs7234341	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs7234798	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs7237879	0.90[ASN][1000 genomes]
rs7239629	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72930222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8084869	0.95[JPT][hapmap]
rs930018	0.95[JPT][hapmap]
rs9635917	0.86[ASN][1000 genomes]
rs9966530	0.91[JPT][hapmap]

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	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1057229	chr18:29335175-29514265	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv2247	chr18:29370842-29415712	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29394400-29418200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29399800-29409400	Weak transcription	HSMMtube	muscle
3	chr18:29400200-29415600	Weak transcription	Brain Angular Gyrus	brain
4	chr18:29401000-29409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr18:29401800-29409400	Weak transcription	HUVEC	blood vessel
6	chr18:29402000-29409400	Weak transcription	Fetal Lung	lung
7	chr18:29402000-29415400	Weak transcription	Right Ventricle	heart
8	chr18:29402200-29409400	Weak transcription	Gastric	stomach
9	chr18:29402200-29414600	Weak transcription	Fetal Heart	heart
10	chr18:29402200-29417200	Weak transcription	Pancreas	Pancrea
11	chr18:29402400-29415400	Weak transcription	Ovary	ovary
12	chr18:29402800-29409400	Weak transcription	Lung	lung
13	chr18:29405200-29413600	Weak transcription	Fetal Stomach	stomach
14	chr18:29405400-29415200	Weak transcription	Small Intestine	intestine
15	chr18:29405600-29409400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:29405600-29412600	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:29405600-29414800	Weak transcription	NH-A	brain
18	chr18:29405600-29481800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:29406000-29409400	Weak transcription	Spleen	Spleen
20	chr18:29406000-29417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
22	chr18:29406600-29409400	Weak transcription	Fetal Muscle Leg	muscle
23	chr18:29406600-29415800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:29406800-29410800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:29406800-29415200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr18:29406800-29431600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr18:29407000-29409400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:29407200-29409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr18:29407200-29409400	Weak transcription	Colonic Mucosa	Colon
30	chr18:29407200-29409400	Weak transcription	NHEK	skin
31	chr18:29407200-29411000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr18:29407200-29411400	Strong transcription	Primary T cells from cord blood	blood
33	chr18:29407200-29414400	Weak transcription	Osteobl	bone
34	chr18:29407200-29415400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:29407400-29410400	Weak transcription	Hela-S3	cervix
36	chr18:29407400-29411000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr18:29407400-29415400	Weak transcription	Fetal Kidney	kidney
38	chr18:29407400-29427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr18:29407400-29429800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr18:29407400-29432000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:29407600-29411000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:29407600-29413600	Weak transcription	Fetal Intestine Small	intestine
43	chr18:29407800-29409400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:29407800-29409400	Weak transcription	Esophagus	oesophagus
45	chr18:29407800-29409400	Weak transcription	Thymus	Thymus
46	chr18:29407800-29410200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr18:29407800-29410400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:29407800-29411600	Strong transcription	Placenta	Placenta
49	chr18:29407800-29413000	Weak transcription	NHLF	lung
50	chr18:29407800-29415000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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