Variant report

Variant	rs9801409
Chromosome Location	chr7:128287109-128287110
allele	A/C
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	chr7:128286599-128288642	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000243302	TF binding region

Extended variants
information (count: 101 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10215560	0.83[EUR][1000 genomes]
rs10215566	0.83[EUR][1000 genomes]
rs10215947	0.83[EUR][1000 genomes]
rs10229874	0.82[EUR][1000 genomes]
rs10237278	0.82[EUR][1000 genomes]
rs10954193	0.82[EUR][1000 genomes]
rs10954194	0.86[EUR][1000 genomes]
rs10954195	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11971248	0.81[EUR][1000 genomes]
rs11977129	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11979586	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12670258	0.83[EUR][1000 genomes]
rs12670271	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12671767	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12672518	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12672529	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12672576	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12672608	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12673048	0.81[EUR][1000 genomes]
rs12673998	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13438170	0.82[EUR][1000 genomes]
rs17169024	0.82[EUR][1000 genomes]
rs17533628	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1809082	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1839593	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1839594	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1970827	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1970828	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2044834	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2402907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34614236	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34648516	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35394926	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3857849	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3896308	0.84[EUR][1000 genomes]
rs3927852	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3931943	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3958079	0.86[AMR][1000 genomes]
rs4077398	0.80[EUR][1000 genomes]
rs4079001	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4079003	0.84[EUR][1000 genomes]
rs4731484	0.81[EUR][1000 genomes]
rs4731486	0.82[EUR][1000 genomes]
rs4731488	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731492	0.82[EUR][1000 genomes]
rs4731493	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4731496	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4731497	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55978216	0.82[EUR][1000 genomes]
rs56052829	0.80[EUR][1000 genomes]
rs56189614	0.81[EUR][1000 genomes]
rs56278047	0.80[EUR][1000 genomes]
rs56916616	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56946745	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57226192	0.81[EUR][1000 genomes]
rs57370656	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58123072	0.83[AMR][1000 genomes]
rs59154282	0.81[EUR][1000 genomes]
rs60229418	0.81[AMR][1000 genomes]
rs61318942	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62479751	0.81[EUR][1000 genomes]
rs62479756	0.80[EUR][1000 genomes]
rs62479757	0.80[EUR][1000 genomes]
rs62481868	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481869	0.84[EUR][1000 genomes]
rs62481873	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481883	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481890	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481892	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481895	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481897	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481901	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62481902	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62481906	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62481907	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62481926	0.83[AMR][1000 genomes]
rs62481939	0.83[EUR][1000 genomes]
rs62481940	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6467188	0.82[EUR][1000 genomes]
rs6467189	0.82[EUR][1000 genomes]
rs6467194	0.81[EUR][1000 genomes]
rs6467195	0.83[EUR][1000 genomes]
rs6467196	0.81[EUR][1000 genomes]
rs6467204	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6467206	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6945532	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6954284	0.81[EUR][1000 genomes]
rs6954404	0.81[EUR][1000 genomes]
rs6969462	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6969554	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6973969	0.83[EUR][1000 genomes]
rs6978887	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236020	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7385007	0.80[EUR][1000 genomes]
rs7781695	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7792915	0.83[EUR][1000 genomes]
rs7793136	0.83[EUR][1000 genomes]
rs9690747	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9690756	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv970938	chr7:128256300-128300276	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs9801409	RP11-274B21.4	cis	Thyroid	GTEx
rs9801409	RP11-274B21.1	cis	Thyroid	GTEx
rs9801409	RP11-274B21.1	cis	Stomach	GTEx
rs9801409	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs9801409	RP11-274B21.4	cis	Stomach	GTEx
rs9801409	RP11-274B21.1	cis	lung	GTEx
rs9801409	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs9801409	RP11-274B21.1	cis	Muscle Skeletal	GTEx
rs9801409	RP11-274B21.4	cis	lung	GTEx
rs9801409	RP11-274B21.2	cis	Artery Tibial	GTEx
rs9801409	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs9801409	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs9801409	RP11-274B21.4	cis	Esophagus Muscularis	GTEx
rs9801409	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs9801409	RP11-274B21.10	cis	Whole Blood	GTEx
rs9801409	RP11-274B21.1	cis	Artery Tibial	GTEx
rs9801409	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9801409	RP11-274B21.2	cis	lung	GTEx
rs9801409	RP11-274B21.1	cis	Artery Aorta	GTEx
rs9801409	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs9801409	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs9801409	RP11-274B21.2	cis	Stomach	GTEx
rs9801409	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs9801409	RP11-274B21.4	cis	Artery Tibial	GTEx
rs9801409	RP11-274B21.4	cis	Whole Blood	GTEx
rs9801409	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs9801409	RP11-274B21.1	cis	Whole Blood	GTEx
rs9801409	RP11-274B21.1	cis	Esophagus Muscularis	GTEx
rs9801409	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs9801409	RP11-274B21.9	cis	Esophagus Mucosa	GTEx
rs9801409	RP11-274B21.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128237800-128290400	Weak transcription	HepG2	liver
2	chr7:128239200-128287200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:128242600-128292800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128249600-128289000	Weak transcription	NHEK	skin
6	chr7:128249600-128293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:128249600-128295200	Weak transcription	NH-A	brain
8	chr7:128249600-128297600	Weak transcription	HUVEC	blood vessel
9	chr7:128249600-128308400	Weak transcription	HSMM	muscle
10	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
11	chr7:128249600-128319600	Weak transcription	NHLF	lung
12	chr7:128252200-128287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:128256800-128288600	Weak transcription	Osteobl	bone
14	chr7:128258600-128287400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:128260000-128296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr7:128260400-128300600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:128262200-128293200	Weak transcription	Brain Germinal Matrix	brain
18	chr7:128265800-128289000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:128266400-128290400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:128267200-128287400	Strong transcription	Fetal Muscle Leg	muscle
21	chr7:128272200-128300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:128272400-128290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:128272400-128290400	Weak transcription	K562	blood
24	chr7:128272400-128292400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:128272400-128293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:128273600-128290600	Weak transcription	Fetal Brain Female	brain
27	chr7:128273800-128291800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:128274200-128296400	Weak transcription	Colonic Mucosa	Colon
29	chr7:128274400-128287400	Strong transcription	Liver	Liver
30	chr7:128274600-128291200	Weak transcription	Esophagus	oesophagus
31	chr7:128275600-128287400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:128275600-128295000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:128275800-128289600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:128276000-128287200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr7:128276000-128287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:128276200-128287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:128277200-128287400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr7:128277400-128287400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr7:128278000-128289000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:128278400-128287400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:128278400-128287600	Strong transcription	Fetal Stomach	stomach
42	chr7:128278400-128288000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:128278400-128289000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:128278600-128287400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:128278800-128287400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:128278800-128287400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr7:128279600-128296200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:128279800-128291200	Weak transcription	Gastric	stomach
49	chr7:128279800-128291800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:128279800-128292600	Weak transcription	Aorta	Aorta

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