Variant report

Variant	rs1048445
Chromosome Location	chr10:99116903-99116904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99115036..99117967-chr10:99132935..99135217,2	K562	blood:
2	chr10:99091407..99096076-chr10:99110583..99117776,8	MCF-7	breast:
3	chr10:99115899..99117497-chr10:99123854..99126044,2	K562	blood:
4	chr10:99115003..99117234-chr10:99118268..99120611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225850	Chromatin interaction
ENSG00000181274	Chromatin interaction
ENSG00000052749	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1048442	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10786336	0.94[ASN][1000 genomes]
rs10786337	0.89[ASN][1000 genomes]
rs10786338	0.87[ASN][1000 genomes]
rs10786339	0.90[ASN][1000 genomes]
rs10786340	0.90[ASN][1000 genomes]
rs10786341	0.88[ASN][1000 genomes]
rs10786342	0.87[ASN][1000 genomes]
rs10786343	0.88[ASN][1000 genomes]
rs10786344	0.83[CHD][hapmap]
rs10786347	0.84[ASN][1000 genomes]
rs10882888	1.00[CHB][hapmap]
rs10882900	0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10882903	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10882907	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10882908	0.95[ASN][1000 genomes]
rs10882909	0.95[ASN][1000 genomes]
rs10882910	0.93[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs10882911	0.95[ASN][1000 genomes]
rs10882912	0.95[ASN][1000 genomes]
rs10882913	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10882914	0.95[ASN][1000 genomes]
rs10882915	0.95[ASN][1000 genomes]
rs10882916	0.90[ASN][1000 genomes]
rs10882917	0.91[ASN][1000 genomes]
rs10882922	0.88[ASN][1000 genomes]
rs10882924	0.87[ASN][1000 genomes]
rs10882926	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10882929	0.83[ASN][1000 genomes]
rs10882930	0.83[ASN][1000 genomes]
rs11189144	0.95[ASN][1000 genomes]
rs11189154	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11189156	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189157	0.85[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189159	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189163	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189165	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11189167	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189168	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11189172	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11189173	0.87[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189174	0.95[ASN][1000 genomes]
rs11189175	0.95[ASN][1000 genomes]
rs11189177	0.95[ASN][1000 genomes]
rs11189178	0.95[ASN][1000 genomes]
rs11189179	0.95[ASN][1000 genomes]
rs11189180	0.95[ASN][1000 genomes]
rs11189181	0.95[ASN][1000 genomes]
rs11189182	0.95[ASN][1000 genomes]
rs11189183	0.95[ASN][1000 genomes]
rs11189191	0.92[ASN][1000 genomes]
rs11189192	0.90[ASN][1000 genomes]
rs11189193	0.88[ASN][1000 genomes]
rs11189195	0.90[ASN][1000 genomes]
rs11189196	0.90[ASN][1000 genomes]
rs11189197	0.88[ASN][1000 genomes]
rs11189200	0.90[ASN][1000 genomes]
rs11189208	0.84[ASN][1000 genomes]
rs11812223	0.87[ASN][1000 genomes]
rs11814021	0.85[ASN][1000 genomes]
rs11817852	0.86[ASN][1000 genomes]
rs11817875	0.86[ASN][1000 genomes]
rs12218483	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12258560	0.94[ASN][1000 genomes]
rs12266723	0.89[ASN][1000 genomes]
rs12359257	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12412478	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12415424	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537645	0.88[ASN][1000 genomes]
rs1537646	0.88[ASN][1000 genomes]
rs1547328	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17112674	0.85[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17112676	1.00[ASN][1000 genomes]
rs17504745	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810983	0.97[ASN][1000 genomes]
rs2275089	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2275090	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2275581	1.00[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[TSI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275582	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297667	0.85[CHD][hapmap]
rs2297668	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2297988	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2861878	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737194	0.83[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3814553	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs3818908	0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs4268448	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635018	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs60237341	0.88[ASN][1000 genomes]
rs61861861	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61861870	0.90[ASN][1000 genomes]
rs61863813	0.98[ASN][1000 genomes]
rs61863815	1.00[ASN][1000 genomes]
rs61863816	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61863819	0.95[ASN][1000 genomes]
rs6584126	0.95[ASN][1000 genomes]
rs6584127	0.95[ASN][1000 genomes]
rs6584128	0.85[CHD][hapmap]
rs7074511	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7074678	0.88[CHB][hapmap]
rs7078004	0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7084654	0.95[ASN][1000 genomes]
rs7088410	0.95[ASN][1000 genomes]
rs7092350	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7092499	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7096801	0.95[ASN][1000 genomes]
rs72838764	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7895695	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7896100	0.90[ASN][1000 genomes]
rs7903847	0.83[ASN][1000 genomes]
rs7905026	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909345	0.90[ASN][1000 genomes]
rs7917752	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7918742	0.99[ASN][1000 genomes]
rs7918948	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921585	1.00[ASN][1000 genomes]
rs7922512	0.90[ASN][1000 genomes]
rs7923385	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7924254	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869967	0.92[ASN][1000 genomes]
rs954149	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9787426	0.90[ASN][1000 genomes]
rs9787454	0.90[ASN][1000 genomes]
rs9887991	0.88[ASN][1000 genomes]
rs9887994	0.88[ASN][1000 genomes]
rs9888026	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9888116	0.88[ASN][1000 genomes]
rs9888117	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1048445	MMS19	cis	cerebellum	SCAN
rs1048445	RRP12	cis	parietal	SCAN
rs1048445	RRP12	cis	Heart Left Ventricle	GTEx
rs1048445	RRP12	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99107000-99131800	Weak transcription	Fetal Kidney	kidney
2	chr10:99107200-99129200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:99107800-99117600	Weak transcription	Fetal Lung	lung
4	chr10:99109000-99157800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:99109400-99118400	Weak transcription	HMEC	breast
6	chr10:99109400-99120400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:99109600-99120600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:99109600-99157800	Strong transcription	Fetal Stomach	stomach
9	chr10:99109800-99118400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:99109800-99118400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:99110200-99118600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:99110400-99118400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:99110600-99132800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:99110800-99139800	Weak transcription	Stomach Mucosa	stomach
15	chr10:99111200-99121600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:99111600-99141800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:99113200-99135400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:99113400-99158600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:99113800-99138800	Strong transcription	Fetal Intestine Small	intestine
20	chr10:99113800-99158800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr10:99113800-99159800	Weak transcription	Fetal Brain Male	brain
22	chr10:99114000-99118200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:99114400-99135000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:99114600-99117400	Strong transcription	Osteobl	bone
25	chr10:99114600-99159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:99114800-99117200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:99115200-99117000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:99115200-99117000	Strong transcription	GM12878-XiMat	blood
29	chr10:99115200-99117200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
30	chr10:99115200-99119200	Strong transcription	Psoas Muscle	Psoas
31	chr10:99115200-99120600	Strong transcription	NHEK	skin
32	chr10:99115200-99120800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:99115200-99127000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:99115200-99133800	Strong transcription	A549	lung
35	chr10:99115200-99134200	Strong transcription	Gastric	stomach
36	chr10:99115200-99136000	Strong transcription	Fetal Brain Female	brain
37	chr10:99115200-99136800	Strong transcription	Dnd41	blood
38	chr10:99115200-99145800	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr10:99115200-99146800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:99115400-99117000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr10:99115400-99117000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr10:99115400-99117400	Genic enhancers	Primary B cells from cord blood	blood
43	chr10:99115400-99117400	Genic enhancers	Primary hematopoietic stem cells	blood
44	chr10:99115400-99117600	Strong transcription	K562	blood
45	chr10:99115400-99119800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr10:99115400-99119800	Strong transcription	NH-A	brain
47	chr10:99115400-99121200	Strong transcription	HepG2	liver
48	chr10:99115400-99121400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:99115400-99134200	Strong transcription	Pancreas	Pancrea
50	chr10:99115400-99157600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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