Variant report

Variant	rs16958610
Chromosome Location	chr18:45425671-45425672
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr18:45425620-45425770	HCM	heart:	n/a	n/a
2	CTCF	chr18:45425580-45425730	SAEC	small airway:	n/a	n/a
3	NFIC	chr18:45424880-45425674	ECC-1	luminal epithelium:	n/a	chr18:45425215-45425232 chr18:45425215-45425231
4	RAD21	chr18:45425369-45425849	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAFK	chr18:45425464-45425947	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr18:45425620-45425770	A549	lung:	n/a	n/a
7	CTCF	chr18:45425560-45425710	HRPEpiC	eye:	n/a	n/a
8	RAD21	chr18:45425479-45425853	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAL1	chr18:45425518-45425843	K562	blood:	n/a	n/a
10	RAD21	chr18:45425460-45425924	MCF-7	breast:	n/a	n/a
11	RAD21	chr18:45425428-45425872	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr18:45425540-45425690	HCPEpiC	choroid plexus:	n/a	n/a
13	CTCF	chr18:45425569-45425748	MCF-7	breast:	n/a	n/a
14	SIN3A	chr18:45425521-45425775	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr18:45425561-45425744	K562	blood:	n/a	n/a
16	CTCF	chr18:45425577-45425685	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr18:45425446-45425757	MCF-7	breast:	n/a	n/a
18	CTCF	chr18:45425560-45425710	HEEpiC	esophagus:	n/a	n/a
19	GTF2F1	chr18:45425503-45425712	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr18:45425560-45425710	WERI-Rb-1	eye:	n/a	n/a
21	CTCF	chr18:45425560-45425710	A549	lung:	n/a	n/a
22	CTCF	chr18:45425560-45425710	HCM	heart:	n/a	n/a
23	CTCF	chr18:45425580-45425730	K562	blood:	n/a	n/a
24	MYC	chr18:45425283-45425799	K562	blood:	n/a	chr18:45425707-45425718
25	USF1	chr18:45425492-45425918	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr18:45425493-45425844	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr18:45425580-45425730	WERI-Rb-1	eye:	n/a	n/a
28	RAD21	chr18:45425546-45425754	A549	lung:	n/a	n/a
29	CTCF	chr18:45425580-45425730	RPTEC	kidney:	n/a	n/a
30	CTCF	chr18:45425640-45425790	MCF-7	breast:	n/a	n/a
31	CTCF	chr18:45425538-45425762	Medullo	brain:	n/a	n/a
32	CTCF	chr18:45425620-45425770	MCF-7	breast:	n/a	n/a
33	CTCF	chr18:45425614-45425690	MCF-7	breast:	n/a	n/a
34	RAD21	chr18:45425475-45425839	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF2	chr18:45425576-45425761	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr18:45425640-45425790	HEEpiC	esophagus:	n/a	n/a
37	CTCF	chr18:45425476-45425819	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:
2	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
3	chr18:45425487..45426123-chr18:45548742..45549619,2	MCF-7	breast:
4	chr18:45424599..45427357-chr18:45454563..45456845,2	K562	blood:
5	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:

No data

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10502889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16958509	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16958575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958602	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes]
rs16958629	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813069	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57631119	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58060476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58573997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58825872	0.95[AMR][1000 genomes]
rs8085335	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs8086227	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs8098413	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9304357	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45397000-45430600	Weak transcription	Brain Angular Gyrus	brain
2	chr18:45400400-45432200	Weak transcription	Ovary	ovary
3	chr18:45401200-45426000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:45409200-45426400	Weak transcription	Fetal Kidney	kidney
5	chr18:45410800-45425800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr18:45410800-45428000	Weak transcription	Aorta	Aorta
7	chr18:45415200-45426000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr18:45417400-45426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr18:45418200-45428400	Weak transcription	Thymus	Thymus
10	chr18:45419600-45428000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:45420000-45426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:45420600-45427000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:45421000-45425800	Genic enhancers	Hela-S3	cervix
16	chr18:45421000-45430600	Weak transcription	Right Ventricle	heart
17	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:45421600-45425800	Weak transcription	Brain Germinal Matrix	brain
19	chr18:45421800-45426600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr18:45421800-45428000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:45421800-45428400	Weak transcription	Psoas Muscle	Psoas
22	chr18:45421800-45430400	Weak transcription	Esophagus	oesophagus
23	chr18:45421800-45430600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr18:45422200-45425800	Weak transcription	GM12878-XiMat	blood
26	chr18:45422200-45429200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr18:45422200-45430600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr18:45422600-45426000	Weak transcription	Fetal Muscle Leg	muscle
29	chr18:45422600-45426400	Weak transcription	Fetal Brain Female	brain
30	chr18:45423000-45430600	Weak transcription	NHLF	lung
31	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:45423200-45425800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:45423200-45426400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr18:45423200-45426400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:45423200-45427600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr18:45423200-45428000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr18:45423200-45428000	Weak transcription	Fetal Thymus	thymus
38	chr18:45423200-45428000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr18:45423200-45428400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:45423200-45428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr18:45423200-45428400	Weak transcription	Spleen	Spleen
42	chr18:45423200-45429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:45423200-45429200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:45423200-45429200	Weak transcription	Right Atrium	heart
45	chr18:45423200-45429200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr18:45423200-45430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr18:45423200-45430600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr18:45423200-45430600	Weak transcription	Left Ventricle	heart
49	chr18:45423200-45430600	Weak transcription	Lung	lung
50	chr18:45423200-45430600	Weak transcription	Pancreas	Pancrea

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