Variant report

Variant	rs7229979
Chromosome Location	chr18:29513836-29513837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:29513413-29513922	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29503480..29506352-chr18:29513383..29515079,3	K562	blood:
2	chr18:29513029..29515925-chr18:29517093..29518613,2	K562	blood:
3	chr18:29503480..29505119-chr18:29513383..29515079,2	K562	blood:
4	chr18:29511145..29516088-chr18:29521483..29523975,5	MCF-7	breast:

Variant related genes	Relation type
RNU6-1050P	TF binding region
ENSG00000153339	Chromatin interaction
ENSG00000263823	Chromatin interaction
ENSG00000222320	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10468902	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1074636	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853415	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853416	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11081730	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11662341	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12604640	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12607426	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12957331	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12969126	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1680643	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1786764	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1815822	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35203717	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826612	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865397	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4513172	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5011500	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521491	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs549818	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs563247	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs614342	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639595	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506944	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6506945	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6506946	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs675570	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67874605	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7230326	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7239098	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7239951	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8084869	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8088396	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8094542	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs930018	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9958368	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9966530	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
2	chr18:29417600-29515600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:29432600-29521400	Weak transcription	Stomach Mucosa	stomach
4	chr18:29461600-29518600	Weak transcription	Psoas Muscle	Psoas
5	chr18:29462000-29520000	Weak transcription	Fetal Heart	heart
6	chr18:29478600-29522000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:29479600-29518600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr18:29480600-29519400	Weak transcription	Spleen	Spleen
9	chr18:29482400-29522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:29482600-29521600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:29482800-29521600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:29484400-29520800	Weak transcription	Fetal Brain Female	brain
13	chr18:29484800-29521000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:29488000-29519600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr18:29490400-29519000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr18:29492600-29519600	Weak transcription	Ovary	ovary
17	chr18:29493000-29521600	Weak transcription	Aorta	Aorta
18	chr18:29493400-29521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr18:29494000-29518400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr18:29496600-29521400	Weak transcription	NHEK	skin
21	chr18:29500600-29521400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr18:29502800-29519400	Weak transcription	GM12878-XiMat	blood
23	chr18:29503000-29518800	Weak transcription	Right Ventricle	heart
24	chr18:29504600-29516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:29505200-29521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr18:29506000-29516800	Strong transcription	Fetal Thymus	thymus
27	chr18:29506800-29521600	Weak transcription	A549	lung
28	chr18:29508000-29515400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:29508000-29515600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr18:29508400-29515600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr18:29508800-29518600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr18:29508800-29520400	Weak transcription	Brain Germinal Matrix	brain
33	chr18:29509000-29519400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr18:29509200-29520800	Weak transcription	Fetal Lung	lung
35	chr18:29509400-29521000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr18:29509600-29514200	Weak transcription	Esophagus	oesophagus
37	chr18:29509600-29514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr18:29509600-29515400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr18:29509600-29517200	Weak transcription	Left Ventricle	heart
40	chr18:29509600-29519400	Weak transcription	Gastric	stomach
41	chr18:29509600-29519400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr18:29509600-29520800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:29509600-29520800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr18:29509600-29522000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr18:29509600-29522000	Weak transcription	Lung	lung
46	chr18:29510000-29520800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr18:29510200-29514200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr18:29510200-29519200	Weak transcription	HepG2	liver
49	chr18:29510200-29519400	Weak transcription	Adipose Nuclei	Adipose
50	chr18:29510200-29521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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