Variant report

Variant	rs7900255
Chromosome Location	chr10:99157575-99157576
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	chr10:99156906-99157641	IMR90	lung:	n/a	n/a
2	POLR2A	chr10:99157482-99157743	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr10:99157400-99157592	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000231970	TF binding region
ENSG00000231508	TF binding region

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1048442	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10786336	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10786337	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10786338	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10786339	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10786340	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10786341	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10786342	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10786343	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10786347	0.85[ASN][1000 genomes]
rs10882908	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882909	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882910	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882911	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882912	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882913	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882914	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882915	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10882916	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10882917	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10882922	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882924	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10882926	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882929	0.86[ASN][1000 genomes]
rs10882930	0.86[ASN][1000 genomes]
rs11189172	0.84[ASN][1000 genomes]
rs11189173	0.84[ASN][1000 genomes]
rs11189174	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189175	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189177	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189178	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189179	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189180	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189181	0.84[ASN][1000 genomes]
rs11189182	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189183	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11189191	0.87[ASN][1000 genomes]
rs11189192	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189193	0.89[ASN][1000 genomes]
rs11189195	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189196	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189197	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11189200	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189208	0.85[ASN][1000 genomes]
rs11812223	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11814021	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11817852	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11817875	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12218483	0.84[ASN][1000 genomes]
rs12258560	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12266723	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12359257	0.84[ASN][1000 genomes]
rs12412478	0.84[ASN][1000 genomes]
rs1537645	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1537646	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2275089	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2275090	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2275582	0.80[ASN][1000 genomes]
rs2297667	0.88[AMR][1000 genomes]
rs2297668	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3814553	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3818787	0.88[AMR][1000 genomes]
rs3818908	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4635018	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60237341	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61861861	0.84[ASN][1000 genomes]
rs61861870	0.89[ASN][1000 genomes]
rs61863816	0.80[ASN][1000 genomes]
rs61863819	0.84[ASN][1000 genomes]
rs6584126	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6584127	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7074511	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7078004	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7084654	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7088410	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7092350	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7092499	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7096801	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72838764	0.84[ASN][1000 genomes]
rs7895695	0.85[ASN][1000 genomes]
rs7896100	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7903562	0.89[AMR][1000 genomes]
rs7903847	0.83[ASN][1000 genomes]
rs7909345	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7916665	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7922512	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs869967	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9787426	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9787454	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9887991	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9887994	0.89[ASN][1000 genomes]
rs9888026	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9888116	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9888117	0.83[AMR][1000 genomes];0.89[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
rs7900255	RRP12	cis	Heart Left Ventricle	GTEx
rs7900255	RP11-452K12.7	cis	Whole Blood	GTEx
rs7900255	RRP12	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99109000-99157800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr10:99109600-99157800	Strong transcription	Fetal Stomach	stomach
3	chr10:99113400-99158600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:99113800-99158800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr10:99113800-99159800	Weak transcription	Fetal Brain Male	brain
6	chr10:99114600-99159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:99115400-99157600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:99115600-99159800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:99115800-99157800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:99115800-99157800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:99115800-99158600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr10:99118000-99159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:99121000-99157600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:99121000-99159600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:99121200-99159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:99122400-99158800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:99122800-99159200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:99127000-99157600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:99127400-99157600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:99127800-99157600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:99128400-99159800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:99129600-99159200	Strong transcription	Osteobl	bone
23	chr10:99130800-99159600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:99131600-99158400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr10:99132000-99157600	Strong transcription	Fetal Muscle Leg	muscle
26	chr10:99136400-99157800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:99141000-99159800	Weak transcription	Stomach Mucosa	stomach
28	chr10:99142200-99159200	Strong transcription	Fetal Intestine Small	intestine
29	chr10:99142800-99157600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:99143000-99157800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr10:99143200-99157600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:99144800-99157600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:99144800-99157600	Strong transcription	Fetal Brain Female	brain
34	chr10:99146600-99158800	Strong transcription	Liver	Liver
35	chr10:99146800-99157600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:99147600-99157600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:99147800-99157600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:99147800-99157600	Strong transcription	HepG2	liver
39	chr10:99148400-99157600	Strong transcription	Left Ventricle	heart
40	chr10:99148400-99159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr10:99150200-99159800	Weak transcription	Fetal Kidney	kidney
42	chr10:99150600-99160000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:99150800-99157600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr10:99150800-99159000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr10:99150800-99159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr10:99150800-99160000	Weak transcription	Esophagus	oesophagus
47	chr10:99151000-99159600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr10:99151000-99160000	Weak transcription	Ovary	ovary
49	chr10:99151200-99159800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr10:99151200-99159800	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links