Variant report

Variant	rs1547328
Chromosome Location	chr10:99109729-99109730
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99102535..99104464-chr10:99107918..99109887,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1048442	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1048445	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786336	0.93[ASN][1000 genomes]
rs10786337	0.88[ASN][1000 genomes]
rs10786338	0.86[ASN][1000 genomes]
rs10786339	0.89[ASN][1000 genomes]
rs10786340	0.89[ASN][1000 genomes]
rs10786341	0.87[ASN][1000 genomes]
rs10786342	0.86[ASN][1000 genomes]
rs10786343	0.87[ASN][1000 genomes]
rs10786344	0.83[CHD][hapmap]
rs10786347	0.84[ASN][1000 genomes]
rs10882888	1.00[CHB][hapmap]
rs10882900	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10882903	0.90[CEU][hapmap];0.83[ASN][1000 genomes]
rs10882904	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10882907	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10882908	0.94[ASN][1000 genomes]
rs10882909	0.94[ASN][1000 genomes]
rs10882910	0.93[CHB][hapmap];0.94[ASN][1000 genomes]
rs10882911	0.94[ASN][1000 genomes]
rs10882912	0.94[ASN][1000 genomes]
rs10882913	0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs10882914	0.94[ASN][1000 genomes]
rs10882915	0.94[ASN][1000 genomes]
rs10882916	0.89[ASN][1000 genomes]
rs10882917	0.90[ASN][1000 genomes]
rs10882922	0.87[ASN][1000 genomes]
rs10882924	0.87[ASN][1000 genomes]
rs10882925	0.84[EUR][1000 genomes]
rs10882926	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10882929	0.83[ASN][1000 genomes]
rs10882930	0.83[ASN][1000 genomes]
rs11189144	0.96[ASN][1000 genomes]
rs11189154	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189155	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11189156	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189157	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189159	0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189163	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189165	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs11189167	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189168	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs11189172	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs11189173	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189174	0.94[ASN][1000 genomes]
rs11189175	0.94[ASN][1000 genomes]
rs11189177	0.94[ASN][1000 genomes]
rs11189178	0.94[ASN][1000 genomes]
rs11189179	0.94[ASN][1000 genomes]
rs11189180	0.94[ASN][1000 genomes]
rs11189181	0.94[ASN][1000 genomes]
rs11189182	0.94[ASN][1000 genomes]
rs11189183	0.94[ASN][1000 genomes]
rs11189191	0.91[ASN][1000 genomes]
rs11189192	0.89[ASN][1000 genomes]
rs11189193	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11189195	0.89[ASN][1000 genomes]
rs11189196	0.89[ASN][1000 genomes]
rs11189197	0.87[ASN][1000 genomes]
rs11189200	0.89[ASN][1000 genomes]
rs11189202	0.83[EUR][1000 genomes]
rs11189208	0.84[ASN][1000 genomes]
rs11812223	0.87[ASN][1000 genomes]
rs11814021	0.84[ASN][1000 genomes]
rs11817852	0.85[ASN][1000 genomes]
rs11817875	0.85[ASN][1000 genomes]
rs12218483	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12258560	0.93[ASN][1000 genomes]
rs12266723	0.88[ASN][1000 genomes]
rs12359257	0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12412478	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12415424	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537645	0.87[ASN][1000 genomes]
rs1537646	0.87[ASN][1000 genomes]
rs17112674	0.86[CEU][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs17112676	0.99[ASN][1000 genomes]
rs17504745	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1810983	0.97[ASN][1000 genomes]
rs2275089	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2275090	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2275581	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275582	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297667	0.85[CHD][hapmap]
rs2297668	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2297988	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2861878	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737194	0.86[CEU][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs3814553	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3818908	0.94[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs4268448	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4635018	0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs60237341	0.87[ASN][1000 genomes]
rs61861861	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61861870	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61863813	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61863815	0.99[ASN][1000 genomes]
rs61863816	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61863818	0.93[EUR][1000 genomes]
rs61863819	0.94[ASN][1000 genomes]
rs6584126	0.94[ASN][1000 genomes]
rs6584127	0.94[ASN][1000 genomes]
rs6584128	0.85[CHD][hapmap]
rs7074511	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs7074678	0.88[CHB][hapmap]
rs7078004	0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7084654	0.94[ASN][1000 genomes]
rs7088410	0.94[ASN][1000 genomes]
rs7092350	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7092499	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7096801	0.94[ASN][1000 genomes]
rs72838764	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7895695	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs7896100	0.89[ASN][1000 genomes]
rs7903847	0.82[ASN][1000 genomes]
rs7905026	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7909345	0.89[ASN][1000 genomes]
rs7917752	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918742	0.98[ASN][1000 genomes]
rs7918948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7921585	0.99[ASN][1000 genomes]
rs7922512	0.89[ASN][1000 genomes]
rs7923385	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs7924254	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869967	0.91[ASN][1000 genomes]
rs954149	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs9787426	0.89[ASN][1000 genomes]
rs9787454	0.89[ASN][1000 genomes]
rs9887991	0.87[ASN][1000 genomes]
rs9887994	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9888026	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9888116	0.87[ASN][1000 genomes]
rs9888117	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv825534	chr10:99081505-99115599	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	esv3516239	chr10:99107769-99110444	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1547328	RRP12	cis	cerebellum	SCAN
rs1547328	RRP12	cis	parietal	SCAN
rs1547328	RRP12	cis	Heart Left Ventricle	GTEx
rs1547328	MMS19	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99095200-99115200	Weak transcription	Gastric	stomach
2	chr10:99095400-99115600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:99095400-99115600	Weak transcription	Left Ventricle	heart
4	chr10:99095400-99115600	Weak transcription	Right Ventricle	heart
5	chr10:99097400-99115200	Weak transcription	A549	lung
6	chr10:99097400-99116000	Weak transcription	Hela-S3	cervix
7	chr10:99097600-99115200	Weak transcription	NHEK	skin
8	chr10:99097600-99115800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:99098200-99116200	Weak transcription	Brain Angular Gyrus	brain
10	chr10:99098400-99115200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:99098600-99114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:99098600-99115400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:99099400-99113600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:99099400-99115600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr10:99101800-99114400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:99102400-99115400	Weak transcription	Pancreas	Pancrea
17	chr10:99103000-99116000	Weak transcription	Brain Germinal Matrix	brain
18	chr10:99104400-99109800	Weak transcription	Primary B cells from cord blood	blood
19	chr10:99105600-99113800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:99106400-99111600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr10:99106600-99113400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:99106800-99116400	Weak transcription	Aorta	Aorta
23	chr10:99107000-99110800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:99107000-99115400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr10:99107000-99131800	Weak transcription	Fetal Kidney	kidney
26	chr10:99107200-99115200	Weak transcription	Psoas Muscle	Psoas
27	chr10:99107200-99115400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:99107200-99115600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr10:99107200-99116000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:99107200-99129200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:99107400-99116000	Weak transcription	Primary T cells from cord blood	blood
32	chr10:99107600-99115200	Weak transcription	Dnd41	blood
33	chr10:99107600-99116000	Weak transcription	Fetal Thymus	thymus
34	chr10:99107800-99114600	Weak transcription	Osteobl	bone
35	chr10:99107800-99117600	Weak transcription	Fetal Lung	lung
36	chr10:99108200-99111200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr10:99108200-99115200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:99108200-99115400	Weak transcription	HepG2	liver
39	chr10:99108200-99116000	Weak transcription	Esophagus	oesophagus
40	chr10:99108400-99111200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:99108400-99115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:99108400-99115800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr10:99108600-99110000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:99108600-99115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:99108600-99115200	Weak transcription	Fetal Brain Female	brain
46	chr10:99108800-99110600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr10:99109000-99115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr10:99109000-99157800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr10:99109200-99109800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:99109200-99109800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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