Variant report

Variant	rs34080686
Chromosome Location	chr1:212527646-212527647
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	chr1:212527545-212528358	K562	blood:	n/a	n/a
2	POLR2A	chr1:212527641-212528072	K562	blood:	n/a	n/a
3	POLR2A	chr1:212527643-212527864	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:212527640-212527651	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212526274..212530393-chr1:212532499..212537435,6	K562	blood:
2	chr1:212526286..212528256-chr1:212589016..212590996,2	K562	blood:

Variant related genes	Relation type
ENSG00000229832	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10863961	0.87[EUR][1000 genomes]
rs10863963	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119919	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119920	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119924	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119929	0.84[ASN][1000 genomes]
rs11119930	0.84[ASN][1000 genomes]
rs11576769	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584189	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585215	0.86[EUR][1000 genomes]
rs11587555	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588867	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590242	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590672	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060029	0.84[ASN][1000 genomes]
rs12062818	0.84[ASN][1000 genomes]
rs12090970	0.88[ASN][1000 genomes]
rs12095810	0.88[ASN][1000 genomes]
rs12411213	0.88[ASN][1000 genomes]
rs12726409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736502	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737825	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743785	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12756678	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470390	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120770	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297306	0.84[ASN][1000 genomes]
rs2358448	0.87[EUR][1000 genomes]
rs2358454	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884465	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884466	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34447409	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35822123	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4951595	0.84[ASN][1000 genomes]
rs55814152	0.86[EUR][1000 genomes]
rs56104831	0.84[ASN][1000 genomes]
rs6661987	0.85[EUR][1000 genomes]
rs6667199	0.86[EUR][1000 genomes]
rs6693849	0.84[EUR][1000 genomes]
rs71646158	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72754339	0.84[ASN][1000 genomes]
rs7518399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968531	0.86[EUR][1000 genomes]
rs968532	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34080686	RP11-15I11.3	cis	lung	GTEx
rs34080686	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs34080686	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs34080686	RP11-15I11.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
4	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
5	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:212502400-212528200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
13	chr1:212505200-212531400	Weak transcription	HMEC	breast
14	chr1:212505800-212533200	Weak transcription	NH-A	brain
15	chr1:212508200-212528000	Weak transcription	Fetal Kidney	kidney
16	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:212514600-212537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:212515000-212528200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:212515000-212528400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:212515000-212528600	Strong transcription	Dnd41	blood
27	chr1:212515200-212536400	Strong transcription	Liver	Liver
28	chr1:212515400-212528600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:212516000-212528600	Strong transcription	Adipose Nuclei	Adipose
30	chr1:212516200-212528400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:212518000-212528000	Weak transcription	NHLF	lung
32	chr1:212518400-212531200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:212519200-212528200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:212520000-212528000	Weak transcription	Osteobl	bone
35	chr1:212522600-212529600	Weak transcription	NHDF-Ad	bronchial
36	chr1:212523600-212528000	Strong transcription	Fetal Intestine Small	intestine
37	chr1:212523600-212528200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
40	chr1:212524400-212528600	Strong transcription	GM12878-XiMat	blood
41	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:212524600-212527800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:212524600-212530800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:212524800-212527800	Strong transcription	Lung	lung
45	chr1:212524800-212528000	Strong transcription	Fetal Stomach	stomach
46	chr1:212525000-212541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:212525200-212528400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:212525400-212528000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:212525400-212528400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:212525400-212528400	Strong transcription	Thymus	Thymus

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