Variant report

Variant	rs9888116
Chromosome Location	chr10:99159482-99159483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr10:99159402-99160598	K562	blood:	n/a	chr10:99160008-99160015
2	POLR2A	chr10:99159011-99161323	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99159358..99162440-chr10:99256931..99260180,3	MCF-7	breast:
2	chr10:99158229..99164055-chr10:99184399..99190088,9	MCF-7	breast:
3	chr10:99158767..99161294-chr10:99204142..99206207,3	K562	blood:
4	chr10:99102792..99105740-chr10:99158426..99160016,2	K562	blood:
5	chr10:99145838..99147761-chr10:99158745..99160617,2	K562	blood:
6	chr10:99149313..99151551-chr10:99158288..99160228,2	MCF-7	breast:
7	chr10:99158733..99161055-chr10:99257726..99260280,2	MCF-7	breast:
8	chr10:99158602..99162553-chr10:99184335..99188453,6	MCF-7	breast:
9	chr10:99158578..99161453-chr10:99205742..99208123,2	MCF-7	breast:
10	chr10:99077463..99079313-chr10:99158629..99160425,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231970	TF binding region
ENSG00000165879	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000224474	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10444013	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10444014	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10444016	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1048442	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048445	0.88[ASN][1000 genomes]
rs10786336	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786337	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786338	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786339	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786340	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786341	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786342	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786343	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786344	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786345	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10786346	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786347	0.96[ASN][1000 genomes]
rs10882900	0.80[ASN][1000 genomes]
rs10882903	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882904	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882907	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882908	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882909	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882910	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882911	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882912	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882913	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882914	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882915	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882916	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882917	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882922	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882924	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882926	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882929	0.95[ASN][1000 genomes]
rs10882930	0.95[ASN][1000 genomes]
rs10882931	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882934	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11189144	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11189156	0.87[ASN][1000 genomes]
rs11189157	0.88[ASN][1000 genomes]
rs11189159	0.88[ASN][1000 genomes]
rs11189163	0.88[ASN][1000 genomes]
rs11189165	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11189167	0.88[ASN][1000 genomes]
rs11189168	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11189172	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189173	0.93[ASN][1000 genomes]
rs11189174	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189175	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189177	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189178	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189179	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189180	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189181	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189182	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189183	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11189191	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189192	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189193	0.97[ASN][1000 genomes]
rs11189195	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189196	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189197	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189200	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189203	0.84[AFR][1000 genomes]
rs11189204	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189206	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189208	0.96[ASN][1000 genomes]
rs11812223	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11814021	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11817852	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11817875	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12218483	0.93[ASN][1000 genomes]
rs12258560	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12266723	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12359257	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12412478	0.93[ASN][1000 genomes]
rs12415424	0.88[ASN][1000 genomes]
rs1537645	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1537646	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1547328	0.87[ASN][1000 genomes]
rs17112674	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17112676	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17504745	0.87[ASN][1000 genomes]
rs1810983	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2275089	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275090	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275581	0.88[ASN][1000 genomes]
rs2275582	0.89[ASN][1000 genomes]
rs2297667	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2297668	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297988	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861878	0.87[ASN][1000 genomes]
rs3737194	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3814553	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818787	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3818908	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4268448	0.87[ASN][1000 genomes]
rs4635018	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60237341	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61861861	0.93[ASN][1000 genomes]
rs61861870	0.98[ASN][1000 genomes]
rs61861912	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61863813	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61863815	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61863816	0.89[ASN][1000 genomes]
rs61863819	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6584126	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6584127	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6584128	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7074511	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7078004	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7078782	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7084654	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7088410	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7092350	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7092499	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7096801	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72838764	0.93[ASN][1000 genomes]
rs7895695	0.96[ASN][1000 genomes]
rs7896100	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900255	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7903562	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7903847	0.91[ASN][1000 genomes]
rs7905026	0.88[ASN][1000 genomes]
rs7909345	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7916665	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7917752	0.87[ASN][1000 genomes]
rs7918742	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7918948	0.88[ASN][1000 genomes]
rs7921585	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7922512	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7923385	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7924254	0.88[ASN][1000 genomes]
rs869967	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs954149	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9787426	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9787454	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9887991	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887994	1.00[ASN][1000 genomes]
rs9888026	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888117	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467437	chr10:99115683-99167436	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv552023	chr10:99115683-99167436	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467438	chr10:99126249-99173870	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv552024	chr10:99126249-99173870	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9888116	RRP12	cis	Heart Left Ventricle	GTEx
rs9888116	RRP12	cis	Muscle Skeletal	GTEx
rs9888116	RP11-452K12.7	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99113800-99159800	Weak transcription	Fetal Brain Male	brain
2	chr10:99115600-99159800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:99118000-99159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:99121000-99159600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr10:99121200-99159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:99128400-99159800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:99130800-99159600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:99141000-99159800	Weak transcription	Stomach Mucosa	stomach
9	chr10:99148400-99159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:99150200-99159800	Weak transcription	Fetal Kidney	kidney
11	chr10:99150600-99160000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:99150800-99159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:99150800-99160000	Weak transcription	Esophagus	oesophagus
14	chr10:99151000-99159600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr10:99151000-99160000	Weak transcription	Ovary	ovary
16	chr10:99151200-99159800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:99151200-99159800	Weak transcription	Colonic Mucosa	Colon
18	chr10:99153400-99159600	Weak transcription	GM12878-XiMat	blood
19	chr10:99153600-99159800	Weak transcription	Brain Substantia Nigra	brain
20	chr10:99153600-99159800	Weak transcription	NHLF	lung
21	chr10:99153800-99160000	Weak transcription	Gastric	stomach
22	chr10:99154400-99159600	Weak transcription	Right Ventricle	heart
23	chr10:99154600-99160000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr10:99154600-99160000	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:99154800-99159800	Weak transcription	Brain Germinal Matrix	brain
26	chr10:99154800-99160000	Weak transcription	Small Intestine	intestine
27	chr10:99156000-99159800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:99156000-99159800	Weak transcription	Fetal Lung	lung
29	chr10:99156200-99159600	Weak transcription	HUVEC	blood vessel
30	chr10:99156200-99159800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:99156200-99159800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:99156200-99159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:99156200-99159800	Weak transcription	NHDF-Ad	bronchial
34	chr10:99156200-99160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:99156200-99160400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:99156400-99159600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:99156400-99159600	Weak transcription	Lung	lung
38	chr10:99156400-99159600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:99156400-99159600	Weak transcription	A549	lung
40	chr10:99156400-99159600	Weak transcription	Hela-S3	cervix
41	chr10:99156400-99159600	Weak transcription	K562	blood
42	chr10:99156400-99159600	Weak transcription	NHEK	skin
43	chr10:99156400-99159800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr10:99156400-99159800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:99156400-99159800	Weak transcription	Adipose Nuclei	Adipose
46	chr10:99156400-99159800	Weak transcription	Brain Angular Gyrus	brain
47	chr10:99156400-99159800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr10:99156400-99159800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:99156400-99159800	Weak transcription	Thymus	Thymus
50	chr10:99156400-99160000	Weak transcription	Spleen	Spleen

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