Variant report

Variant	rs2448116
Chromosome Location	chr10:26985438-26985439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:26985213-26988196	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr10:26985416-26988207	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr10:26985115-26986834	U87	brain:	n/a	n/a
4	POLR2A	chr10:26985173-26987271	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:26985003-26986784	K562	blood:	n/a	n/a
6	SREBP2	chr10:26985363-26987338	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:26985174-26987321	GM19099	blood:	n/a	n/a
8	POLR2A	chr10:26985126-26986809	U87	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26985323..26988042-chr10:27148387..27150466,3	MCF-7	breast:
2	chr10:26985057..26986781-chr10:27006850..27009579,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABI1-7	chr10:26984020-26986554	NONHSAT011856

No data

Variant related genes	Relation type
PDSS1	TF binding region
ENSG00000136754	Chromatin interaction
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10764634	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1613801	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1616471	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677711	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1677713	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1677714	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1677715	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677726	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1677727	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677731	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1677732	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1677733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677735	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1677736	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1677737	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1677738	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1677739	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1748338	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1748340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1748343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748345	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748346	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1748347	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1748348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1748349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748350	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1748351	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17558625	0.81[ASN][1000 genomes]
rs17558709	0.83[ASN][1000 genomes]
rs1780170	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1780171	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780172	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1780173	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1780175	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1780177	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1780178	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1780185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1780187	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1780188	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1809358	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1812155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1824851	0.93[ASN][1000 genomes]
rs1871299	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1871300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005118	0.85[EUR][1000 genomes]
rs2005119	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2005253	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251814	0.83[EUR][1000 genomes]
rs2254745	0.82[ASN][1000 genomes]
rs2448109	0.86[EUR][1000 genomes]
rs2448110	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2448112	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2448113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2448115	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2448118	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2448119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2448120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448121	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2448122	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448123	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2448124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2448125	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2448126	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2448128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2448129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2448131	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2477278	0.80[ASN][1000 genomes]
rs2477282	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2477283	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2477285	0.83[EUR][1000 genomes]
rs2477286	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2477287	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2477288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477289	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477290	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477293	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489556	0.82[ASN][1000 genomes]
rs2489558	0.83[EUR][1000 genomes]
rs2489560	0.80[ASN][1000 genomes]
rs2489584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489585	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2489586	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489590	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489591	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489592	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2489593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489594	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2489595	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2489596	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2489597	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489598	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2489600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489602	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2489603	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2860415	0.88[EUR][1000 genomes]
rs2887183	0.82[ASN][1000 genomes]
rs2985471	0.82[ASN][1000 genomes]
rs2996641	0.82[ASN][1000 genomes]
rs3101794	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3118157	0.82[ASN][1000 genomes]
rs3118159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3118160	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3121616	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3121618	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4749176	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7905832	0.85[EUR][1000 genomes]
rs7910625	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7914153	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7916511	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs899374	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9417486	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9418574	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2448116	PDSS1	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26978800-26985600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr10:26978800-26985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr10:26980200-26985600	Weak transcription	Fetal Thymus	thymus
4	chr10:26983800-26985600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:26983800-26985600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:26983800-26985600	Weak transcription	HSMM	muscle
7	chr10:26983800-26985600	Weak transcription	NHEK	skin
8	chr10:26984000-26985600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:26984200-26985600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr10:26984200-26985600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:26984400-26985600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:26985000-26985600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr10:26985000-26985600	Enhancers	Thymus	Thymus
14	chr10:26985200-26985600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr10:26985200-26985600	Enhancers	K562	blood
16	chr10:26985400-26985600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:26985400-26985600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr10:26985400-26985600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr10:26985400-26985600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:26985400-26985600	Enhancers	Primary T cells from cord blood	blood
21	chr10:26985400-26985600	Enhancers	Primary hematopoietic stem cells	blood
22	chr10:26985400-26985600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr10:26985400-26985600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr10:26985400-26985600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr10:26985400-26985600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:26985400-26985600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:26985400-26985600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:26985400-26985600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr10:26985400-26985600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:26985400-26985600	Enhancers	Brain Substantia Nigra	brain
31	chr10:26985400-26985600	Enhancers	Duodenum Mucosa	Duodenum
32	chr10:26985400-26985600	Enhancers	Fetal Brain Female	brain
33	chr10:26985400-26985600	Enhancers	Fetal Heart	heart
34	chr10:26985400-26985600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr10:26985400-26985600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr10:26985400-26985600	Enhancers	Rectal Smooth Muscle	rectum
37	chr10:26985400-26985600	Enhancers	Stomach Mucosa	stomach
38	chr10:26985400-26985600	Enhancers	Hela-S3	cervix
39	chr10:26985400-26985600	Enhancers	HMEC	breast
40	chr10:26985400-26986000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr10:26985400-26986000	Flanking Active TSS	Dnd41	blood
42	chr10:26985400-26986200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr10:26985400-26988600	Active TSS	GM12878-XiMat	blood

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