Variant report

Variant	rs9429171
Chromosome Location	chr1:46090679-46090680
allele	C/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	chr1:46090598-46090815	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:46090624-46090811	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:46088530-46090808	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46088002..46091701-chr1:46094509..46096362,4	K562	blood:
2	chr1:46048860..46051215-chr1:46089890..46092822,3	K562	blood:
3	chr1:46048178..46050215-chr1:46089233..46091590,2	K562	blood:

Variant related genes	Relation type
CCDC17	TF binding region
ENSG00000159592	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10430105	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10749856	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10789467	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10789468	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789470	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890333	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10890334	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10890335	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10890336	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10890337	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890340	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890341	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10890342	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10890343	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890344	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211145	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211146	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211147	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211149	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211151	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11211152	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211157	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211158	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211159	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211160	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211161	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211162	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211163	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11211165	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211166	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211168	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211169	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211170	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11211171	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1135812	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1135850	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12022673	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12023439	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12024590	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12025613	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12027622	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12037459	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12037803	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12041197	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041677	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12043945	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12045096	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12045451	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12047629	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12048866	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12049027	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12070775	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081175	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12091503	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1250	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1541131	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1547924	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1547925	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1972410	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2050376	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2152078	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2230658	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2230659	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2253862	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275085	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2275086	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370457	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28442079	0.80[EUR][1000 genomes]
rs28623463	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991977	0.89[EUR][1000 genomes]
rs2991978	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991979	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991981	0.89[EUR][1000 genomes]
rs2991983	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2991986	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2991987	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2991988	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2991989	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3014210	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3014212	0.89[EUR][1000 genomes]
rs3014234	0.83[AMR][1000 genomes]
rs3014235	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3014236	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3014237	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3014239	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3014240	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014242	0.87[AMR][1000 genomes]
rs3014245	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3014246	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3014248	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3014249	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014251	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3811435	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3811436	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4415615	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4431884	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4439382	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4559551	0.81[AMR][1000 genomes]
rs4564187	0.81[AMR][1000 genomes]
rs4586014	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4607935	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4609469	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4660313	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660879	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4660880	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61784793	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61784795	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61784796	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6429574	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6429575	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658700	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6662164	0.80[EUR][1000 genomes]
rs6665808	0.83[EUR][1000 genomes]
rs66682726	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6686944	0.81[EUR][1000 genomes]
rs6690926	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6694889	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6699418	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6699444	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703748	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7529699	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7545118	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7547414	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8179296	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8179402	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9429172	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9793568	0.84[AMR][1000 genomes];0.84[EUR][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	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9429171	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs9429171	GPBP1L1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46071200-46093000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:46074800-46108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:46076200-46094000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:46077800-46112600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:46078200-46101200	Strong transcription	Thymus	Thymus
10	chr1:46078400-46100800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:46078800-46101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:46079000-46100600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:46079600-46094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:46079800-46109800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:46082000-46090800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:46083200-46093000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:46083200-46094000	Weak transcription	Small Intestine	intestine
18	chr1:46083400-46095000	Weak transcription	Stomach Mucosa	stomach
19	chr1:46083600-46091400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:46083600-46091800	Weak transcription	Brain Substantia Nigra	brain
21	chr1:46083600-46093800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:46083800-46092400	Weak transcription	NHDF-Ad	bronchial
23	chr1:46083800-46093600	Weak transcription	Aorta	Aorta
24	chr1:46084000-46093600	Weak transcription	Fetal Brain Male	brain
25	chr1:46084200-46093200	Weak transcription	Hela-S3	cervix
26	chr1:46084200-46093600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:46084200-46093600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:46084400-46091200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:46084400-46091400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:46084400-46091400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:46084400-46093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:46084400-46094800	Weak transcription	Fetal Kidney	kidney
33	chr1:46084600-46092800	Weak transcription	NH-A	brain
34	chr1:46085000-46091400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:46085000-46091600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:46085200-46093600	Weak transcription	Psoas Muscle	Psoas
37	chr1:46085400-46091400	Weak transcription	HMEC	breast
38	chr1:46085800-46091400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:46085800-46093400	Weak transcription	HepG2	liver
40	chr1:46086000-46096000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:46086400-46091400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:46086600-46091200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:46087000-46091400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:46087400-46091400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
46	chr1:46088000-46094400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:46088200-46095200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:46088200-46110000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:46088400-46091800	Weak transcription	Fetal Lung	lung
50	chr1:46088400-46093400	Weak transcription	HUVEC	blood vessel

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