Variant report

Variant	rs11817875
Chromosome Location	chr10:99158414-99158415
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	chr10:99158408-99158674	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99158229..99164055-chr10:99184399..99190088,9	MCF-7	breast:
2	chr10:99149313..99151551-chr10:99158288..99160228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231970	TF binding region
ENSG00000052749	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000171314	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10444013	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10444014	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10444016	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1048442	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048445	0.86[ASN][1000 genomes]
rs10786336	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10786337	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786338	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786339	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786340	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786341	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786342	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786343	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786344	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786345	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10786346	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786347	0.92[ASN][1000 genomes]
rs10882903	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10882904	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882907	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882908	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882909	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882910	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882911	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882912	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882913	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882914	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882915	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882916	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882917	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882922	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882924	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882926	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882929	0.91[ASN][1000 genomes]
rs10882930	0.91[ASN][1000 genomes]
rs10882931	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882934	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11189144	0.81[ASN][1000 genomes]
rs11189156	0.84[ASN][1000 genomes]
rs11189157	0.86[ASN][1000 genomes]
rs11189159	0.86[ASN][1000 genomes]
rs11189163	0.86[ASN][1000 genomes]
rs11189165	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11189167	0.86[ASN][1000 genomes]
rs11189168	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11189172	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189173	0.91[ASN][1000 genomes]
rs11189174	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189175	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189177	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189178	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189179	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189180	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189181	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189182	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189183	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189191	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189192	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189193	0.94[ASN][1000 genomes]
rs11189195	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189196	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189197	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189200	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189203	0.84[AFR][1000 genomes]
rs11189204	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189206	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189208	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11812223	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11814021	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11817852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12218483	0.91[ASN][1000 genomes]
rs12258560	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12266723	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12359257	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12412478	0.91[ASN][1000 genomes]
rs12415424	0.86[ASN][1000 genomes]
rs1537645	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537646	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547328	0.85[ASN][1000 genomes]
rs17112674	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17112676	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17504745	0.84[ASN][1000 genomes]
rs1810983	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2275089	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275090	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275581	0.86[ASN][1000 genomes]
rs2275582	0.87[ASN][1000 genomes]
rs2297667	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2297668	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297988	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2861878	0.85[ASN][1000 genomes]
rs3737194	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3814553	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818787	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3818908	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4268448	0.84[ASN][1000 genomes]
rs4635018	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60237341	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61861861	0.91[ASN][1000 genomes]
rs61861870	0.96[ASN][1000 genomes]
rs61861912	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61863813	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61863815	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61863816	0.87[ASN][1000 genomes]
rs61863819	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6584126	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6584127	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6584128	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7074511	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7078004	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078782	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7084654	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7088410	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7092350	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7092499	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7096801	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72838764	0.91[ASN][1000 genomes]
rs7895695	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7896100	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7900255	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7903562	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7903847	0.88[ASN][1000 genomes]
rs7905026	0.86[ASN][1000 genomes]
rs7909345	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7916665	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7917752	0.85[ASN][1000 genomes]
rs7918742	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7918948	0.86[ASN][1000 genomes]
rs7921585	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7922512	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7923385	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7924254	0.85[ASN][1000 genomes]
rs869967	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs954149	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787426	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787454	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9887991	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9887994	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9888026	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9888116	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9888117	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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
rs11817875	RRP12	cis	Muscle Skeletal	GTEx
rs11817875	RRP12	cis	Heart Left Ventricle	GTEx
rs11817875	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	chr10:99113400-99158600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:99113800-99158800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:99113800-99159800	Weak transcription	Fetal Brain Male	brain
4	chr10:99114600-99159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:99115600-99159800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr10:99115800-99158600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr10:99118000-99159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:99121000-99159600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:99121200-99159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:99122400-99158800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:99122800-99159200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:99128400-99159800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr10:99129600-99159200	Strong transcription	Osteobl	bone
14	chr10:99130800-99159600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:99141000-99159800	Weak transcription	Stomach Mucosa	stomach
16	chr10:99142200-99159200	Strong transcription	Fetal Intestine Small	intestine
17	chr10:99146600-99158800	Strong transcription	Liver	Liver
18	chr10:99148400-99159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:99150200-99159800	Weak transcription	Fetal Kidney	kidney
20	chr10:99150600-99160000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr10:99150800-99159000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:99150800-99159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:99150800-99160000	Weak transcription	Esophagus	oesophagus
24	chr10:99151000-99159600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:99151000-99160000	Weak transcription	Ovary	ovary
26	chr10:99151200-99159800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr10:99151200-99159800	Weak transcription	Colonic Mucosa	Colon
28	chr10:99152800-99158800	Strong transcription	NH-A	brain
29	chr10:99153000-99158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:99153400-99159600	Weak transcription	GM12878-XiMat	blood
31	chr10:99153600-99159800	Weak transcription	Brain Substantia Nigra	brain
32	chr10:99153600-99159800	Weak transcription	NHLF	lung
33	chr10:99153800-99160000	Weak transcription	Gastric	stomach
34	chr10:99154400-99159600	Weak transcription	Right Ventricle	heart
35	chr10:99154600-99160000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr10:99154600-99160000	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:99154800-99159800	Weak transcription	Brain Germinal Matrix	brain
38	chr10:99154800-99160000	Weak transcription	Small Intestine	intestine
39	chr10:99156000-99159800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr10:99156000-99159800	Weak transcription	Fetal Lung	lung
41	chr10:99156200-99159600	Weak transcription	HUVEC	blood vessel
42	chr10:99156200-99159800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:99156200-99159800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:99156200-99159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:99156200-99159800	Weak transcription	NHDF-Ad	bronchial
46	chr10:99156200-99160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:99156200-99160400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:99156400-99158800	Weak transcription	Pancreas	Pancrea
49	chr10:99156400-99159600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:99156400-99159600	Weak transcription	Lung	lung

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