Variant report

Variant	rs28678901
Chromosome Location	chr15:44081143-44081144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:44080628-44082076	Raji	blood:	n/a	n/a
2	POLR2A	chr15:44080827-44081888	GM12878	blood:	n/a	n/a
3	TBP	chr15:44080791-44081158	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:44081031..44082541-chr15:44082800..44084359,2	K562	blood:
2	15:44001645-44015047..15:44080886-44089111	Hela-S3	cervix:
3	chr15:44065408..44074556-chr15:44080543..44088380,28	MCF-7	breast:
4	chr15:44068786..44071554-chr15:44078288..44081551,3	MCF-7	breast:
5	chr15:44080256..44082677-chr15:44153726..44155422,2	MCF-7	breast:

No data

Variant related genes	Relation type
SERF2	TF binding region
ENSG00000242866	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000238494	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000166763	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10163054	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10438303	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11070407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11070408	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070410	0.93[ASN][1000 genomes]
rs11852840	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856495	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11856795	0.81[AMR][1000 genomes]
rs11857661	0.82[EUR][1000 genomes]
rs12101756	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12437808	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440573	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441127	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441861	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441984	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442129	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12443102	0.81[EUR][1000 genomes]
rs12702	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899922	0.86[ASN][1000 genomes]
rs13380397	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16950562	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16963953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16965120	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16977724	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16977798	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1965794	0.82[ASN][1000 genomes]
rs1965795	0.89[ASN][1000 genomes]
rs2228368	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2277531	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2412810	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2447193	0.81[EUR][1000 genomes]
rs2447208	0.81[EUR][1000 genomes]
rs2447211	0.81[EUR][1000 genomes]
rs2447212	0.81[EUR][1000 genomes]
rs2467402	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2467426	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2470121	0.81[EUR][1000 genomes]
rs2788	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28377539	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28413704	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28433760	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28476182	0.88[ASN][1000 genomes]
rs28502289	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28504496	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28509275	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28513374	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28519630	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28524541	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28531819	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28542007	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28546844	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28564774	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28578041	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28578398	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28583806	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28590651	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28595038	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28606452	0.81[EUR][1000 genomes]
rs28636829	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28674750	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28679673	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28684672	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28687459	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28696802	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28707214	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28718261	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28780699	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28781888	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28823973	0.81[ASN][1000 genomes]
rs28866846	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28891769	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927075	0.82[EUR][1000 genomes]
rs2955969	0.93[ASN][1000 genomes]
rs2957637	0.81[EUR][1000 genomes]
rs35457073	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736180	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742982	0.84[EUR][1000 genomes]
rs3759790	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759791	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784275	0.85[EUR][1000 genomes]
rs3816792	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825783	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4332723	0.85[ASN][1000 genomes]
rs4997480	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56008017	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56909447	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs575082	0.94[ASN][1000 genomes]
rs57865312	0.81[EUR][1000 genomes]
rs60883262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61390361	0.81[AMR][1000 genomes]
rs62018952	1.00[ASN][1000 genomes]
rs68079546	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs688009	0.83[ASN][1000 genomes]
rs693919	0.94[ASN][1000 genomes]
rs694461	0.94[ASN][1000 genomes]
rs7168158	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169322	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169382	0.94[ASN][1000 genomes]
rs7169988	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7170167	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170751	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171750	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174208	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7175032	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175129	0.85[ASN][1000 genomes]
rs7179388	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7180818	0.95[ASN][1000 genomes]
rs7183809	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72714307	0.91[AMR][1000 genomes]
rs8023696	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029210	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8030169	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8032649	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033995	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8040839	0.91[ASN][1000 genomes]
rs8042868	0.82[EUR][1000 genomes]
rs9989313	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS 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 miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats 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 miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28678901	CKMT1A	cis	Skin Sun Exposed Lower leg	GTEx
rs28678901	ADAL	cis	Thyroid	GTEx
rs28678901	ADAL	cis	Nerve Tibial	GTEx
rs28678901	ADAL	cis	Artery Tibial	GTEx
rs28678901	CATSPER2	cis	Whole Blood	GTEx
rs28678901	CATSPER2	cis	Esophagus Mucosa	GTEx
rs28678901	ADAL	cis	Esophagus Muscularis	GTEx
rs28678901	ADAL	cis	lung	GTEx
rs28678901	AC011330.5	cis	Esophagus Mucosa	GTEx
rs28678901	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28678901	CKMT1A	cis	Esophagus Mucosa	GTEx
rs28678901	ADAL	cis	Stomach	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44070200-44083800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:44070200-44083800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:44070200-44083800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:44070200-44083800	Weak transcription	NHDF-Ad	bronchial
5	chr15:44070200-44083800	Weak transcription	NHEK	skin
6	chr15:44070600-44083600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:44070600-44083800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:44070800-44083600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr15:44071600-44083600	Weak transcription	Dnd41	blood
10	chr15:44071600-44083600	Weak transcription	Hela-S3	cervix
11	chr15:44071600-44083800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:44076800-44083600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:44079400-44081400	Weak transcription	Pancreas	Pancrea
14	chr15:44079800-44083800	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:44080200-44081400	Enhancers	Primary B cells from cord blood	blood
16	chr15:44080400-44081800	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:44080600-44082000	Enhancers	K562	blood
18	chr15:44080600-44083800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:44080800-44081600	Enhancers	Placenta	Placenta
20	chr15:44080800-44083600	Weak transcription	Fetal Intestine Large	intestine
21	chr15:44080800-44083600	Weak transcription	Stomach Mucosa	stomach
22	chr15:44081000-44081400	Enhancers	GM12878-XiMat	blood
23	chr15:44081000-44083600	Weak transcription	Fetal Intestine Small	intestine
24	chr15:44081000-44083800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:44081000-44083800	Weak transcription	Stomach Smooth Muscle	stomach

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