Variant report

Variant	rs12028730
Chromosome Location	chr1:45922116-45922117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45804302..45805997-chr1:45921545..45923744,2	K562	blood:
2	chr1:45186398..45188731-chr1:45921034..45922679,2	K562	blood:
3	chr1:45834804..45837730-chr1:45920539..45922621,2	K562	blood:

Variant related genes	Relation type
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006215	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007859	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10493120	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11211110	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211113	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211114	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211115	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211116	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582197	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582198	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583290	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032658	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12048023	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1691216	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1691217	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1691218	0.84[AMR][1000 genomes]
rs1691221	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1765710	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1765711	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771549	0.84[AMR][1000 genomes]
rs2642901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28789981	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6429566	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669989	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781057	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781059	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs781060	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781061	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781062	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781063	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781065	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription 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	191 gene(s)	inside rSNPs	diseases
2	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12028730	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs12028730	CCDC163P	cis	lung	GTEx
rs12028730	CCDC163P	cis	Thyroid	GTEx
rs12028730	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12028730	CCDC163P	cis	Artery Aorta	GTEx
rs12028730	CCDC163P	cis	Artery Tibial	GTEx
rs12028730	CCDC163P	cis	Whole Blood	GTEx
rs12028730	CCDC163P	cis	Stomach	GTEx
rs12028730	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12028730	CCDC163P	cis	Nerve Tibial	GTEx
rs12028730	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12028730	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12028730	CCDC163P	cis	Muscle Skeletal	GTEx
rs12028730	CCDC163P	cis	Heart Left Ventricle	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:45902600-45924200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:45909000-45924600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:45909200-45922400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:45911000-45930400	Weak transcription	Psoas Muscle	Psoas
6	chr1:45911400-45924400	Weak transcription	Placenta	Placenta
7	chr1:45912800-45922400	Weak transcription	Liver	Liver
8	chr1:45912800-45923800	Weak transcription	HepG2	liver
9	chr1:45913000-45931000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:45913000-45933000	Weak transcription	Ovary	ovary
11	chr1:45915400-45924000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:45915400-45924800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:45915400-45940600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45915600-45929600	Weak transcription	Left Ventricle	heart
15	chr1:45915800-45923200	Weak transcription	Fetal Stomach	stomach
16	chr1:45917000-45924000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:45917000-45930000	Weak transcription	Aorta	Aorta
18	chr1:45917200-45923800	Weak transcription	Spleen	Spleen
19	chr1:45919000-45941000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:45920600-45923400	Strong transcription	Primary B cells from cord blood	blood
21	chr1:45920600-45932600	Weak transcription	GM12878-XiMat	blood
22	chr1:45920800-45922400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:45920800-45923200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:45921200-45923200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:45921200-45924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:45921200-45924600	Weak transcription	Brain Angular Gyrus	brain
27	chr1:45921200-45924600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:45921200-45933800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:45921200-45934200	Weak transcription	Brain Substantia Nigra	brain
30	chr1:45921400-45922400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:45921400-45922400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:45921400-45924800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:45921600-45924000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:45921800-45933000	Weak transcription	Primary B cells from peripheral blood	blood

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