Variant report

Variant	rs1053941
Chromosome Location	chr1:46084383-46084384
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46077998..46080201-chr1:46083457..46085148,2	K562	blood:
2	chr1:46082896..46084867-chr1:46088374..46090403,2	MCF-7	breast:
3	chr1:46076715..46080031-chr1:46084203..46087065,4	K562	blood:
4	chr1:46084077..46086305-chr1:46151131..46152894,2	K562	blood:
5	chr1:45185928..45188614-chr1:46083047..46085498,2	K562	blood:
6	chr1:46083627..46085575-chr1:46092823..46094633,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000159588	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11579176	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11582058	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11585275	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587918	0.86[EUR][1000 genomes]
rs11587982	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11590549	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs12042481	1.00[ASW][hapmap]
rs2065708	0.81[GIH][hapmap];0.85[MEX][hapmap]
rs28412451	0.87[EUR][1000 genomes]
rs28433203	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs28484896	0.85[EUR][1000 genomes]
rs28584711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3014232	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310432	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423055	1.00[CHB][hapmap]
rs4434876	1.00[CHB][hapmap]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55659201	0.85[EUR][1000 genomes]
rs55951835	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020747	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067046	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56093189	0.82[EUR][1000 genomes]
rs56238114	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251392	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs58692133	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429573	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429579	1.00[CHB][hapmap]
rs6662572	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6662999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671239	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6702764	1.00[CHB][hapmap]
rs72688452	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688460	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517111	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525281	1.00[CHB][hapmap]
rs7541935	0.81[EUR][1000 genomes]
rs7553374	1.00[ASN][1000 genomes]
rs9429173	0.81[AMR][1000 genomes];0.86[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

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1053941	CCDC163P	cis	Esophagus Muscularis	GTEx
rs1053941	CCDC163P	cis	Artery Tibial	GTEx
rs1053941	CCDC163P	cis	lung	GTEx
rs1053941	CCDC163P	cis	Thyroid	GTEx
rs1053941	CCDC163P	cis	Heart Left Ventricle	GTEx
rs1053941	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs1053941	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs1053941	CCDC163P	cis	Muscle Skeletal	GTEx
rs1053941	CYP4A11	cis	parietal	SCAN
rs1053941	CCDC163P	cis	Artery Aorta	GTEx
rs1053941	MED8	cis	cerebellum	SCAN
rs1053941	CCDC163P	cis	Nerve Tibial	GTEx
rs1053941	CCDC163P	cis	Stomach	GTEx
rs1053941	CCDC163P	cis	Esophagus Mucosa	GTEx
rs1053941	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs1053941	CCDC163P	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052800-46086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:46052800-46089200	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:46053600-46086000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:46055000-46085200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:46055200-46090400	Strong transcription	Dnd41	blood
8	chr1:46066800-46084400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:46066800-46086800	Strong transcription	K562	blood
10	chr1:46067000-46086400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:46067200-46086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:46067200-46087400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:46067400-46086600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:46068000-46086600	Strong transcription	Placenta	Placenta
15	chr1:46068200-46085000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:46068200-46086600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:46068200-46087000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:46068200-46087400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr1:46068200-46087400	Strong transcription	Fetal Thymus	thymus
20	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:46071000-46087400	Strong transcription	Fetal Stomach	stomach
22	chr1:46071200-46093000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:46071600-46087200	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:46072200-46084400	Strong transcription	Fetal Lung	lung
26	chr1:46074600-46084800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:46074600-46087400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:46074800-46108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:46075200-46086400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:46075400-46087400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:46075600-46088000	Weak transcription	Fetal Heart	heart
32	chr1:46075600-46088000	Strong transcription	Fetal Intestine Small	intestine
33	chr1:46075800-46087200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:46076200-46094000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:46077800-46084800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:46077800-46085800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:46077800-46086400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:46077800-46086400	Strong transcription	Fetal Intestine Large	intestine
39	chr1:46077800-46086600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:46077800-46088200	Strong transcription	Primary T cells from cord blood	blood
41	chr1:46077800-46090000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:46077800-46090200	Strong transcription	Fetal Brain Female	brain
43	chr1:46077800-46112600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:46078000-46084400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:46078000-46085200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:46078000-46085200	Strong transcription	A549	lung
47	chr1:46078000-46087600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:46078200-46084400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:46078200-46084400	Strong transcription	HepG2	liver
50	chr1:46078200-46084600	Strong transcription	Left Ventricle	heart

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