Variant report

Variant	rs2554328
Chromosome Location	chr15:52153573-52153574
allele	C/G/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	MAX	chr15:52153334-52153609	K562	blood:	n/a	chr15:52153532-52153539
2	POLR2A	chr15:52153340-52153588	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52120607..52125174-chr15:52151783..52155506,6	MCF-7	breast:

Variant related genes	Relation type
TMOD3	TF binding region
ENSG00000259632	TF binding region
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 266 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:264)

rs_ID	r²[population]
rs1025184	0.92[EUR][1000 genomes]
rs1035737	0.93[EUR][1000 genomes]
rs1035739	0.87[EUR][1000 genomes]
rs10444824	0.90[EUR][1000 genomes]
rs10444825	0.89[EUR][1000 genomes]
rs10851503	0.99[EUR][1000 genomes]
rs10851504	0.96[EUR][1000 genomes]
rs11049	0.91[EUR][1000 genomes]
rs11070866	0.83[EUR][1000 genomes]
rs11070867	0.83[EUR][1000 genomes]
rs11070868	0.89[EUR][1000 genomes]
rs11070869	0.89[EUR][1000 genomes]
rs1135871	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630253	0.92[EUR][1000 genomes]
rs11630579	0.91[EUR][1000 genomes]
rs11630943	0.89[EUR][1000 genomes]
rs11631858	0.89[EUR][1000 genomes]
rs11636869	0.94[EUR][1000 genomes]
rs11637876	0.93[EUR][1000 genomes]
rs11638677	0.91[EUR][1000 genomes]
rs12050524	0.89[EUR][1000 genomes]
rs12591672	0.96[EUR][1000 genomes]
rs12593708	0.99[EUR][1000 genomes]
rs12901638	0.96[EUR][1000 genomes]
rs12902346	0.83[EUR][1000 genomes]
rs12903500	0.81[EUR][1000 genomes]
rs12904413	0.89[EUR][1000 genomes]
rs12904900	0.88[EUR][1000 genomes]
rs12905283	0.94[EUR][1000 genomes]
rs12908327	0.98[EUR][1000 genomes]
rs12912928	0.94[EUR][1000 genomes]
rs12913583	0.93[EUR][1000 genomes]
rs12913850	0.99[EUR][1000 genomes]
rs12915015	0.98[EUR][1000 genomes]
rs12915568	0.98[EUR][1000 genomes]
rs17526463	0.93[EUR][1000 genomes]
rs17526760	0.98[EUR][1000 genomes]
rs17539905	0.92[EUR][1000 genomes]
rs17610862	0.89[EUR][1000 genomes]
rs17611193	0.93[EUR][1000 genomes]
rs17612102	0.87[EUR][1000 genomes]
rs17612123	0.90[EUR][1000 genomes]
rs1811326	0.89[AMR][1000 genomes]
rs1840708	0.84[EUR][1000 genomes]
rs1863430	0.93[EUR][1000 genomes]
rs1867984	0.89[AMR][1000 genomes]
rs1972689	0.85[AMR][1000 genomes]
rs2006772	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2006773	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007335	0.99[EUR][1000 genomes]
rs2007355	0.99[EUR][1000 genomes]
rs2010026	0.87[EUR][1000 genomes]
rs2011995	0.98[EUR][1000 genomes]
rs2014638	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2034856	0.89[EUR][1000 genomes]
rs2052705	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2052706	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2052708	0.98[EUR][1000 genomes]
rs2052709	0.95[EUR][1000 genomes]
rs2114191	0.90[EUR][1000 genomes]
rs2241503	0.87[EUR][1000 genomes]
rs2251135	0.83[EUR][1000 genomes]
rs2252606	0.93[EUR][1000 genomes]
rs2252831	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253116	0.94[EUR][1000 genomes]
rs2264339	0.87[AMR][1000 genomes]
rs2414119	0.80[AMR][1000 genomes]
rs2414122	0.91[EUR][1000 genomes]
rs2433217	0.94[EUR][1000 genomes]
rs2433221	0.92[EUR][1000 genomes]
rs2433222	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2436655	0.93[EUR][1000 genomes]
rs2436656	0.96[EUR][1000 genomes]
rs2436657	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436658	0.93[EUR][1000 genomes]
rs2436660	0.92[EUR][1000 genomes]
rs2436661	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2436662	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441780	0.93[EUR][1000 genomes]
rs2448946	0.95[EUR][1000 genomes]
rs2448947	0.93[EUR][1000 genomes]
rs2448948	0.95[EUR][1000 genomes]
rs2448949	0.90[EUR][1000 genomes]
rs2448950	0.95[EUR][1000 genomes]
rs2448951	0.95[EUR][1000 genomes]
rs2448953	0.91[EUR][1000 genomes]
rs2470590	0.83[EUR][1000 genomes]
rs2470591	0.83[EUR][1000 genomes]
rs2470600	0.95[EUR][1000 genomes]
rs2470601	0.93[EUR][1000 genomes]
rs2470602	0.93[EUR][1000 genomes]
rs2470603	0.87[EUR][1000 genomes]
rs2470604	0.82[EUR][1000 genomes]
rs2470605	0.86[EUR][1000 genomes]
rs2470607	0.86[EUR][1000 genomes]
rs2470608	0.95[EUR][1000 genomes]
rs2470610	0.93[EUR][1000 genomes]
rs2470611	0.92[EUR][1000 genomes]
rs2470612	0.91[EUR][1000 genomes]
rs2470616	0.92[EUR][1000 genomes]
rs2470618	0.94[EUR][1000 genomes]
rs2470619	0.88[AMR][1000 genomes]
rs2554305	0.85[AMR][1000 genomes]
rs2554306	0.85[AMR][1000 genomes]
rs2554307	0.85[AMR][1000 genomes]
rs2554308	0.85[AMR][1000 genomes]
rs2554314	0.92[EUR][1000 genomes]
rs2554322	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2554327	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554332	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2554334	0.89[AMR][1000 genomes]
rs2554336	0.89[AMR][1000 genomes]
rs2554337	0.83[EUR][1000 genomes]
rs2554342	0.94[EUR][1000 genomes]
rs2554345	0.89[AMR][1000 genomes]
rs2554348	0.84[ASN][1000 genomes]
rs2554349	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2554350	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2554353	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570224	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570228	0.89[AMR][1000 genomes]
rs2570231	0.83[AMR][1000 genomes]
rs2570233	0.86[AMR][1000 genomes]
rs2570235	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2570236	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570237	0.85[AMR][1000 genomes]
rs2570238	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2570239	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570240	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570241	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570248	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570251	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570252	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570253	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570258	0.90[AMR][1000 genomes]
rs2570260	0.90[AMR][1000 genomes]
rs2570263	0.94[EUR][1000 genomes]
rs2570268	0.94[EUR][1000 genomes]
rs2570269	0.93[EUR][1000 genomes]
rs2570271	0.93[EUR][1000 genomes]
rs2570275	0.93[EUR][1000 genomes]
rs2593168	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593170	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2593173	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2593177	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2593179	0.95[EUR][1000 genomes]
rs2593182	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2593183	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2593185	0.93[EUR][1000 genomes]
rs2593187	0.93[EUR][1000 genomes]
rs2593188	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2593191	0.89[AMR][1000 genomes]
rs2593194	0.83[EUR][1000 genomes]
rs2593198	0.93[EUR][1000 genomes]
rs2593199	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2593202	0.93[EUR][1000 genomes]
rs2593204	0.87[EUR][1000 genomes]
rs2623243	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2623244	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623254	0.85[AMR][1000 genomes]
rs2623255	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623259	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2623262	0.89[AMR][1000 genomes]
rs2623266	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623271	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623279	0.95[EUR][1000 genomes]
rs2623281	0.95[EUR][1000 genomes]
rs2623282	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623283	0.95[EUR][1000 genomes]
rs2623284	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623285	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623286	0.95[EUR][1000 genomes]
rs2623288	0.94[EUR][1000 genomes]
rs2623289	0.94[EUR][1000 genomes]
rs2912186	0.96[EUR][1000 genomes]
rs2912187	0.91[EUR][1000 genomes]
rs2912188	0.91[EUR][1000 genomes]
rs2912189	0.94[EUR][1000 genomes]
rs2916169	0.96[EUR][1000 genomes]
rs2916170	0.93[EUR][1000 genomes]
rs2916171	0.93[EUR][1000 genomes]
rs2916172	0.93[EUR][1000 genomes]
rs2916175	0.95[EUR][1000 genomes]
rs2916176	0.95[EUR][1000 genomes]
rs2916177	0.92[EUR][1000 genomes]
rs2921951	0.93[EUR][1000 genomes]
rs2921953	0.93[EUR][1000 genomes]
rs2921957	0.81[EUR][1000 genomes]
rs2929422	0.91[EUR][1000 genomes]
rs2929423	0.96[EUR][1000 genomes]
rs2929424	0.91[EUR][1000 genomes]
rs2929425	0.93[EUR][1000 genomes]
rs2929426	0.93[EUR][1000 genomes]
rs2929428	0.92[EUR][1000 genomes]
rs2959285	0.94[EUR][1000 genomes]
rs2959289	0.89[EUR][1000 genomes]
rs2959291	0.91[EUR][1000 genomes]
rs2959292	0.91[EUR][1000 genomes]
rs2959293	0.91[EUR][1000 genomes]
rs2959298	0.93[EUR][1000 genomes]
rs2959299	0.93[EUR][1000 genomes]
rs2959300	0.93[EUR][1000 genomes]
rs2959302	0.92[EUR][1000 genomes]
rs2959304	0.90[EUR][1000 genomes]
rs2959305	0.95[EUR][1000 genomes]
rs2959306	0.95[EUR][1000 genomes]
rs2959307	0.94[EUR][1000 genomes]
rs3110551	0.84[EUR][1000 genomes]
rs3110553	0.83[EUR][1000 genomes]
rs34504520	0.89[EUR][1000 genomes]
rs34842090	0.83[EUR][1000 genomes]
rs35270232	0.93[EUR][1000 genomes]
rs35823585	0.91[EUR][1000 genomes]
rs36087956	0.93[EUR][1000 genomes]
rs3751596	0.80[AMR][1000 genomes]
rs3794532	0.89[EUR][1000 genomes]
rs4365237	0.85[EUR][1000 genomes]
rs4775983	0.80[AMR][1000 genomes]
rs56148956	0.89[EUR][1000 genomes]
rs56185947	0.90[EUR][1000 genomes]
rs62015190	0.88[EUR][1000 genomes]
rs62016192	0.96[EUR][1000 genomes]
rs6493520	0.91[EUR][1000 genomes]
rs6493521	0.88[EUR][1000 genomes]
rs6493523	0.84[AMR][1000 genomes]
rs6493525	0.94[EUR][1000 genomes]
rs6493526	0.95[EUR][1000 genomes]
rs7162176	0.83[EUR][1000 genomes]
rs7162554	0.93[EUR][1000 genomes]
rs7162925	0.94[EUR][1000 genomes]
rs7163541	0.93[EUR][1000 genomes]
rs7164961	0.90[EUR][1000 genomes]
rs7170091	0.91[EUR][1000 genomes]
rs7170910	0.96[EUR][1000 genomes]
rs7171516	0.91[EUR][1000 genomes]
rs7171796	0.93[EUR][1000 genomes]
rs7174497	0.85[EUR][1000 genomes]
rs7174808	0.85[EUR][1000 genomes]
rs7175017	0.84[EUR][1000 genomes]
rs7178166	0.85[EUR][1000 genomes]
rs7178561	0.94[EUR][1000 genomes]
rs7178776	0.93[EUR][1000 genomes]
rs7178940	0.91[EUR][1000 genomes]
rs7179599	0.90[EUR][1000 genomes]
rs7181540	0.83[EUR][1000 genomes]
rs726158	0.89[EUR][1000 genomes]
rs72732914	0.95[EUR][1000 genomes]
rs8024585	0.94[EUR][1000 genomes]
rs8025069	0.85[EUR][1000 genomes]
rs8026521	0.93[EUR][1000 genomes]
rs8027721	0.84[EUR][1000 genomes]
rs8028486	0.93[EUR][1000 genomes]
rs8028922	0.89[EUR][1000 genomes]
rs8029036	0.90[EUR][1000 genomes]
rs8031045	0.98[ASN][1000 genomes]
rs8033433	0.95[EUR][1000 genomes]
rs8035126	0.96[EUR][1000 genomes]
rs8038344	0.98[EUR][1000 genomes]
rs8040975	0.85[EUR][1000 genomes]
rs8040991	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041866	0.82[EUR][1000 genomes]
rs919059	0.89[AMR][1000 genomes]
rs990665	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9944235	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2554328	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:52135800-52155000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:52136000-52155200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:52136200-52155000	Weak transcription	Aorta	Aorta
6	chr15:52137800-52155000	Weak transcription	Fetal Intestine Large	intestine
7	chr15:52138000-52155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:52138600-52155000	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
10	chr15:52139400-52156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:52139600-52154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:52139800-52153600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:52140000-52155000	Weak transcription	NH-A	brain
14	chr15:52140200-52155400	Weak transcription	HSMMtube	muscle
15	chr15:52140400-52155000	Weak transcription	HSMM	muscle
16	chr15:52140600-52155400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:52141400-52155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:52141600-52155000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
20	chr15:52141800-52154000	Weak transcription	Adipose Nuclei	Adipose
21	chr15:52141800-52155000	Weak transcription	Fetal Stomach	stomach
22	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:52142200-52155400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:52144200-52155000	Weak transcription	K562	blood
25	chr15:52145000-52156600	Weak transcription	Fetal Brain Female	brain
26	chr15:52145400-52153800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:52145600-52155000	Weak transcription	Placenta	Placenta
28	chr15:52145800-52154000	Weak transcription	Left Ventricle	heart
29	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
30	chr15:52146400-52153600	Weak transcription	Small Intestine	intestine
31	chr15:52146600-52155200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:52147400-52155000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:52147600-52153800	Weak transcription	Gastric	stomach
34	chr15:52148000-52155000	Weak transcription	Osteobl	bone
35	chr15:52148200-52155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52148200-52157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:52148400-52155200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:52148600-52155000	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:52148600-52155000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:52149000-52161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:52149200-52155400	Weak transcription	Ovary	ovary
43	chr15:52149200-52156200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:52149400-52154800	Weak transcription	NHLF	lung
45	chr15:52149400-52155000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:52149400-52156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
48	chr15:52149600-52155000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:52149600-52155000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:52149600-52155000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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