Variant report

Variant	rs9429091
Chromosome Location	chr1:46513088-46513089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46511778..46513975-chr1:46596807..46598312,2	K562	blood:
2	chr1:46512594..46514721-chr1:46598820..46600667,2	MCF-7	breast:
3	chr1:46511398..46513219-chr1:46661327..46664273,2	K562	blood:
4	chr1:46509486..46511609-chr1:46512647..46514463,2	K562	blood:

Variant related genes	Relation type
ENSG00000085998	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10749861	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789482	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890379	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11211247	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11580953	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11584814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11587648	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11805376	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12047120	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1355641	0.85[EUR][1000 genomes]
rs17855317	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2067635	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3795318	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4256763	0.82[EUR][1000 genomes]
rs4300171	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4382655	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4388641	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4420029	0.85[EUR][1000 genomes]
rs4524993	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4660330	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4660333	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4660901	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4660909	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55641506	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55652826	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55735913	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55765474	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56047133	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56140667	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56295206	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56301932	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56368769	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6429590	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6429592	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6429593	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6669534	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6685465	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6687316	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6689417	0.82[EUR][1000 genomes]
rs6693222	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696284	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6700322	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72677518	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72677530	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72677533	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72677541	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72677543	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72677545	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72677546	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72677550	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72677553	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72690901	0.82[EUR][1000 genomes]
rs72692603	0.82[EUR][1000 genomes]
rs72692632	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72692639	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7512448	0.81[EUR][1000 genomes]
rs7530480	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7532388	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7533750	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7552810	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7555458	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884443	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9429090	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9429093	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9429179	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9429184	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9429187	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9429188	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1007750	chr1:46471293-46552564	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9429091	CCDC163P	cis	Muscle Skeletal	GTEx
rs9429091	CCDC163P	cis	Whole Blood	GTEx
rs9429091	CCDC163P	cis	Stomach	GTEx
rs9429091	CCDC163P	cis	Nerve Tibial	GTEx
rs9429091	CCDC163P	cis	Artery Tibial	GTEx
rs9429091	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs9429091	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs9429091	CCDC163P	cis	lung	GTEx
rs9429091	CCDC163P	cis	Esophagus Mucosa	GTEx
rs9429091	CCDC163P	cis	Heart Left Ventricle	GTEx
rs9429091	CCDC163P	cis	Artery Aorta	GTEx
rs9429091	CCDC163P	cis	Esophagus Muscularis	GTEx
rs9429091	CCDC163P	cis	Thyroid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46475600-46525000	Weak transcription	Fetal Kidney	kidney
2	chr1:46476600-46515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:46490200-46524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46490600-46525200	Weak transcription	NH-A	brain
5	chr1:46498000-46528200	Weak transcription	Osteobl	bone
6	chr1:46498200-46528400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:46501000-46525200	Weak transcription	Gastric	stomach
8	chr1:46501400-46548200	Weak transcription	Aorta	Aorta
9	chr1:46501600-46523600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:46503400-46535600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:46505000-46514200	Strong transcription	Dnd41	blood
12	chr1:46505400-46531000	Weak transcription	HUVEC	blood vessel
13	chr1:46505600-46518600	Weak transcription	K562	blood
14	chr1:46505600-46527800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:46505600-46537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:46506000-46549400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:46506200-46518800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:46506200-46528200	Weak transcription	Liver	Liver
19	chr1:46507000-46523600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:46507000-46523800	Weak transcription	Lung	lung
21	chr1:46507400-46513400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:46508000-46526600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:46508000-46528600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:46508200-46519200	Weak transcription	Right Ventricle	heart
25	chr1:46508200-46526400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:46508400-46536200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:46508400-46546600	Weak transcription	HSMMtube	muscle
28	chr1:46508800-46526600	Weak transcription	Fetal Brain Male	brain
29	chr1:46508800-46534200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:46508800-46537400	Weak transcription	HMEC	breast
31	chr1:46509000-46514000	Weak transcription	Fetal Heart	heart
32	chr1:46509000-46524800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:46509200-46523800	Weak transcription	Thymus	Thymus
34	chr1:46509400-46519000	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:46509400-46521000	Weak transcription	Brain Germinal Matrix	brain
36	chr1:46509400-46523600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:46509400-46524000	Weak transcription	Fetal Thymus	thymus
38	chr1:46509600-46513200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:46509600-46521200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:46509600-46522400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:46509600-46524800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:46509600-46526600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:46509600-46526800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:46509600-46527000	Weak transcription	Brain Angular Gyrus	brain
45	chr1:46509600-46528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:46509600-46529000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:46509600-46540200	Weak transcription	Spleen	Spleen
48	chr1:46509800-46515400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:46509800-46523600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:46509800-46526000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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