Variant report

Variant	rs12966444
Chromosome Location	chr18:9123632-9123633
allele	A/G
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	chr18:9123517-9123850	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:9123467-9123866	HepG2	liver:	n/a	n/a
3	POLR2A	chr18:9123551-9123769	MCF-7	breast:	n/a	n/a
4	TCF7L2	chr18:9123606-9123650	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:9123518-9123874	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr18:9123579-9123836	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9123369..9127442-chr18:9129820..9133797,5	MCF-7	breast:
2	chr18:9115568..9117749-chr18:9121152..9124030,3	MCF-7	breast:
3	chr18:9120335..9122312-chr18:9122344..9126216,3	MCF-7	breast:

Variant related genes	Relation type
NDUFV2	TF binding region
ENSG00000266053	Chromatin interaction
ENSG00000263847	Chromatin interaction
ENSG00000178127	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1034486	0.86[YRI][hapmap]
rs1046491	0.92[ASW][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs10502390	0.89[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10853373	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11081459	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11081463	0.92[ASW][hapmap];0.89[CEU][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11081469	0.86[YRI][hapmap]
rs11660889	0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs11661901	0.85[YRI][hapmap]
rs11661921	0.86[YRI][hapmap];0.80[AMR][1000 genomes]
rs11663175	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs11663949	0.89[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs11872176	0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs11872481	0.89[CEU][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11875086	0.90[AMR][1000 genomes]
rs11876775	0.90[AMR][1000 genomes]
rs11876821	0.92[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs11877843	0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs12454025	0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12454497	0.86[YRI][hapmap]
rs12454908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12454936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12455304	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs12457266	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12457429	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12956041	0.87[GIH][hapmap]
rs12966775	0.89[CEU][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12968060	0.89[CEU][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35002591	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35587943	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35774167	0.93[AMR][1000 genomes]
rs35849084	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41274300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62085924	0.84[AMR][1000 genomes]
rs62085926	0.84[AMR][1000 genomes]
rs6506641	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6506647	0.86[YRI][hapmap]
rs71362073	0.84[AMR][1000 genomes]
rs7226632	0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs7229685	0.89[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs8085549	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs8085669	0.87[AMR][1000 genomes]
rs8086362	1.00[YRI][hapmap]
rs8089577	0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs8090297	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8095601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv543641	chr18:9120450-9181498	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3497732	chr18:9121988-9124378	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3497733	chr18:9121988-9124378	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9104400-9130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9107000-9135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:9107400-9135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:9107800-9134600	Weak transcription	Fetal Brain Male	brain
5	chr18:9108200-9127200	Weak transcription	Fetal Brain Female	brain
6	chr18:9111200-9125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr18:9111600-9126800	Weak transcription	Colonic Mucosa	Colon
8	chr18:9114000-9127400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:9114000-9130800	Weak transcription	Ovary	ovary
10	chr18:9115400-9134600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr18:9115800-9134800	Strong transcription	Dnd41	blood
12	chr18:9116800-9135200	Strong transcription	Fetal Thymus	thymus
13	chr18:9117200-9134800	Weak transcription	Brain Germinal Matrix	brain
14	chr18:9117400-9125800	Weak transcription	Right Atrium	heart
15	chr18:9117400-9132000	Strong transcription	Fetal Intestine Large	intestine
16	chr18:9117400-9135200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr18:9117400-9135600	Weak transcription	Esophagus	oesophagus
18	chr18:9117400-9135800	Weak transcription	Gastric	stomach
19	chr18:9117600-9127400	Weak transcription	Spleen	Spleen
20	chr18:9117600-9134800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr18:9117600-9135200	Weak transcription	Psoas Muscle	Psoas
22	chr18:9117600-9135800	Weak transcription	Pancreas	Pancrea
23	chr18:9117800-9124000	Strong transcription	HepG2	liver
24	chr18:9117800-9127200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:9117800-9128800	Weak transcription	Lung	lung
26	chr18:9117800-9132600	Weak transcription	Aorta	Aorta
27	chr18:9117800-9135000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr18:9117800-9135600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:9117800-9135800	Weak transcription	Small Intestine	intestine
30	chr18:9118200-9124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr18:9118200-9134400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr18:9118200-9135000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:9118400-9134400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:9118600-9123800	Strong transcription	Fetal Kidney	kidney
35	chr18:9118600-9123800	Strong transcription	Hela-S3	cervix
36	chr18:9118600-9134600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr18:9118600-9135000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr18:9118800-9124000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr18:9118800-9124000	Strong transcription	Osteobl	bone
40	chr18:9118800-9134400	Strong transcription	K562	blood
41	chr18:9118800-9135600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr18:9118800-9135600	Weak transcription	Right Ventricle	heart
43	chr18:9119000-9124200	Strong transcription	Placenta	Placenta
44	chr18:9119000-9132600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr18:9119200-9123800	Strong transcription	NHLF	lung
46	chr18:9119200-9125200	Weak transcription	Fetal Heart	heart
47	chr18:9119200-9131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr18:9119200-9134400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr18:9119400-9135200	Weak transcription	Stomach Mucosa	stomach
50	chr18:9119600-9124000	Strong transcription	Rectal Mucosa Donor 29	rectum

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