Variant report

Variant	rs11189204
Chromosome Location	chr10:99164394-99164395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99163654..99167601-chr10:99201565..99206372,5	MCF-7	breast:
2	chr10:99163386..99166099-chr10:99171495..99174383,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171307	Chromatin interaction
ENSG00000171311	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10444013	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444014	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444016	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048442	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786336	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10786337	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786338	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10786339	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10786340	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10786341	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786342	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786343	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10786344	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786345	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786346	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786347	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10882903	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882904	0.84[EUR][1000 genomes]
rs10882907	0.85[EUR][1000 genomes]
rs10882908	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10882909	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882910	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882911	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882912	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882913	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882914	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882915	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10882917	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10882922	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882924	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882926	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882929	0.83[AMR][1000 genomes]
rs10882930	0.83[AMR][1000 genomes]
rs10882931	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882934	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189144	0.81[EUR][1000 genomes]
rs11189165	0.85[EUR][1000 genomes]
rs11189168	0.85[EUR][1000 genomes]
rs11189172	0.88[EUR][1000 genomes]
rs11189174	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189175	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189177	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189178	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189179	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189180	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11189181	0.84[EUR][1000 genomes]
rs11189182	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11189183	0.87[EUR][1000 genomes]
rs11189191	0.90[EUR][1000 genomes]
rs11189192	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189195	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189196	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189197	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189200	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189206	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189208	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11812223	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11814021	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11817852	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11817875	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12258560	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12266723	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12359257	0.88[EUR][1000 genomes]
rs1537645	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1537646	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17112674	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17112676	0.85[EUR][1000 genomes]
rs1810983	0.83[EUR][1000 genomes]
rs1932001	0.80[AMR][1000 genomes]
rs2275089	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2275090	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2297667	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297668	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2297988	0.84[EUR][1000 genomes]
rs3737194	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814553	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818787	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818908	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4635018	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60237341	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61861912	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61863813	0.80[EUR][1000 genomes]
rs61863815	0.85[EUR][1000 genomes]
rs61863819	0.88[EUR][1000 genomes]
rs6584126	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6584127	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6584128	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7074511	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078004	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078782	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084654	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7088410	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092350	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092499	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7096801	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7895695	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7896100	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7903562	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7909345	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7918742	0.82[EUR][1000 genomes]
rs7921585	0.83[EUR][1000 genomes]
rs7922512	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7923385	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs869967	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954149	0.85[EUR][1000 genomes]
rs9787426	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9787454	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9887991	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9888026	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9888116	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9888117	0.94[AMR][1000 genomes];0.95[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11189204	RRP12	cis	Muscle Skeletal	GTEx
rs11189204	RRP12	cis	Heart Left Ventricle	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161200-99167000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:99161200-99167000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:99161400-99165800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:99161400-99165800	Weak transcription	K562	blood
5	chr10:99161400-99166000	Weak transcription	NHEK	skin
6	chr10:99161400-99166400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:99161400-99166400	Weak transcription	A549	lung
8	chr10:99161400-99167000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:99161400-99167000	Weak transcription	Liver	Liver
10	chr10:99161600-99165200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:99161600-99165400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:99161600-99165600	Weak transcription	Adipose Nuclei	Adipose
13	chr10:99161600-99165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:99161600-99166000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:99161600-99166000	Weak transcription	Hela-S3	cervix
16	chr10:99161600-99166400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:99161600-99166400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr10:99161600-99166800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:99161600-99166800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr10:99161600-99166800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr10:99161600-99166800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:99161600-99166800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:99161600-99166800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:99161600-99166800	Weak transcription	Fetal Intestine Small	intestine
25	chr10:99161600-99167000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:99161600-99167000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:99161600-99167000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:99161600-99167000	Weak transcription	Brain Substantia Nigra	brain
29	chr10:99161600-99167000	Weak transcription	Fetal Muscle Leg	muscle
30	chr10:99161600-99167000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:99161600-99167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:99161600-99167000	Weak transcription	Dnd41	blood
33	chr10:99161600-99167200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:99161600-99167200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:99161600-99167200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:99161600-99167200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:99161600-99167200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr10:99161600-99167200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:99161600-99167200	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:99161600-99167200	Weak transcription	Fetal Heart	heart
41	chr10:99161600-99167200	Weak transcription	Left Ventricle	heart
42	chr10:99161600-99167200	Weak transcription	Right Atrium	heart
43	chr10:99161600-99167200	Weak transcription	Spleen	Spleen
44	chr10:99161600-99178800	Weak transcription	Fetal Stomach	stomach
45	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
46	chr10:99161800-99164800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:99161800-99165400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:99161800-99166600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:99161800-99166800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:99161800-99167000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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