Variant report

Variant	rs7517111
Chromosome Location	chr1:46122140-46122141
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	STAT3	chr1:46122103-46122142	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr1:46121901-46122450	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46113919..46122142-chr1:46149927..46154523,9	K562	blood:
2	chr1:46118216..46120545-chr1:46121839..46124168,2	K562	blood:

Variant related genes	Relation type
GPBP1L1	TF binding region
ENSG00000234329	TF binding region
ENSG00000159596	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1053941	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579176	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11585275	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587918	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11587982	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11590549	0.89[EUR][1000 genomes]
rs28412451	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28433203	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28484896	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28584711	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3014232	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310432	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[ASN][1000 genomes]
rs55659201	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55951835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020747	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067046	1.00[ASN][1000 genomes]
rs56093189	0.90[EUR][1000 genomes]
rs56238114	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251392	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs58692133	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6662999	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671239	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72688452	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688460	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541935	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7553374	1.00[ASN][1000 genomes]
rs9429173	0.91[AMR][1000 genomes];0.95[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	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
2	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
3	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
4	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
5	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
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7517111	CCDC163P	cis	Stomach	GTEx
rs7517111	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs7517111	CCDC163P	cis	Heart Left Ventricle	GTEx
rs7517111	CCDC163P	cis	Whole Blood	GTEx
rs7517111	CCDC163P	cis	lung	GTEx
rs7517111	CCDC163P	cis	Nerve Tibial	GTEx
rs7517111	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs7517111	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs7517111	CCDC163P	cis	Thyroid	GTEx
rs7517111	CCDC163P	cis	Muscle Skeletal	GTEx
rs7517111	CCDC163P	cis	Esophagus Mucosa	GTEx
rs7517111	CCDC163P	cis	Esophagus Muscularis	GTEx
rs7517111	TMEM69	Cis_1M	lymphoblastoid	RTeQTL
rs7517111	CCDC163P	cis	Artery Aorta	GTEx
rs7517111	CCDC163P	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
3	chr1:46088600-46127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46089600-46126400	Strong transcription	Primary T cells from cord blood	blood
5	chr1:46089800-46127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:46091000-46126400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:46091200-46127000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:46091200-46127000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:46091200-46127200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:46091200-46128200	Strong transcription	Dnd41	blood
11	chr1:46091400-46127000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:46091400-46127000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:46091400-46127000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:46093200-46127000	Strong transcription	K562	blood
15	chr1:46097200-46126800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:46098400-46133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:46100200-46135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:46106200-46140000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:46110600-46122400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:46111400-46122200	Strong transcription	GM12878-XiMat	blood
21	chr1:46111400-46126200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:46111400-46126400	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:46111400-46126800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:46111600-46126000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:46112600-46126800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:46112600-46127000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:46112800-46126800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:46113000-46126600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:46113000-46126800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:46113000-46127000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:46113200-46127000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:46113200-46128000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:46113600-46122200	Strong transcription	Liver	Liver
34	chr1:46113600-46124600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:46113600-46126000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:46113800-46126400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:46113800-46126800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:46113800-46127000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:46113800-46127000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:46113800-46127000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:46113800-46127000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:46113800-46127000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:46113800-46133400	Weak transcription	Right Atrium	heart
44	chr1:46114000-46126600	Strong transcription	Placenta	Placenta
45	chr1:46114000-46127400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:46114000-46129200	Strong transcription	Primary B cells from cord blood	blood
47	chr1:46114200-46126400	Strong transcription	Adipose Nuclei	Adipose
48	chr1:46114200-46127000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:46114400-46123400	Weak transcription	Stomach Mucosa	stomach
50	chr1:46114600-46126000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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