Variant report

Variant	rs7553465
Chromosome Location	chr1:93644410-93644411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:93643938-93644557	MCF10A-Er-Src	breast:	n/a	n/a
2	ARID3A	chr1:93644176-93644483	K562	blood:	n/a	n/a
3	MXI1	chr1:93643106-93647204	SK-N-SH	brain:	n/a	n/a
4	BHLHE40	chr1:93643968-93644493	HepG2	liver:	n/a	n/a
5	MAZ	chr1:93643854-93644681	IMR90	lung:	n/a	n/a
6	CHD1	chr1:93643454-93647252	IMR90	lung:	n/a	chr1:93645456-93645466

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93643262..93645748-chr1:94311384..94313517,2	K562	blood:
2	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
3	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
4	chr1:93643769..93645748-chr1:94311324..94312884,2	K562	blood:
5	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
6	chr1:93542817..93546420-chr1:93641583..93645468,3	MCF-7	breast:
7	chr1:93631724..93634968-chr1:93643710..93645431,3	K562	blood:
8	chr1:93592377..93594266-chr1:93643687..93645200,2	K562	blood:
9	chr1:93296314..93299115-chr1:93644282..93648010,4	K562	blood:

No data

Variant related genes	Relation type
CCDC18	TF binding region
ENSG00000251795	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000143033	Chromatin interaction
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1000607	0.86[EUR][1000 genomes]
rs1057257	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060622	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874759	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10874762	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874764	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874772	0.86[EUR][1000 genomes]
rs10874773	0.86[EUR][1000 genomes]
rs1088318	0.83[ASN][1000 genomes]
rs11164870	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11164871	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164876	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164880	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164902	0.86[EUR][1000 genomes]
rs12030549	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038699	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12044657	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12118230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128131	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12130734	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12139009	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12385720	0.84[AMR][1000 genomes]
rs1335679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474927	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1535699	0.85[EUR][1000 genomes]
rs1537758	0.89[ASN][1000 genomes]
rs1572343	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1856027	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1932314	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967721	0.86[ASN][1000 genomes]
rs2031225	0.85[EUR][1000 genomes]
rs2031226	0.85[EUR][1000 genomes]
rs2152358	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208044	0.83[AMR][1000 genomes]
rs2295423	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2295424	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296558	0.82[ASN][1000 genomes]
rs2297707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391254	0.86[EUR][1000 genomes]
rs2765545	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783489	0.89[ASN][1000 genomes]
rs35940311	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754184	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754186	0.83[ASN][1000 genomes]
rs4240966	0.86[EUR][1000 genomes]
rs4847235	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847398	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847399	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847401	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847402	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847408	0.86[EUR][1000 genomes]
rs4847410	0.85[EUR][1000 genomes]
rs531358	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531514	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs535760	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs547866	0.83[ASN][1000 genomes]
rs555161	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565919	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs569414	0.86[EUR][1000 genomes]
rs602204	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs612037	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61799471	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs622608	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs624131	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627779	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs637646	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541401	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6541404	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6680107	0.85[EUR][1000 genomes]
rs6682670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688230	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703310	0.86[EUR][1000 genomes]
rs682514	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs687394	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs693737	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7418101	0.81[ASN][1000 genomes]
rs7512911	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7513705	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517363	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524964	0.84[EUR][1000 genomes]
rs7526112	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7532195	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7532549	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7535628	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7537403	0.86[EUR][1000 genomes]
rs7539307	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540025	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7541304	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7541687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547244	0.86[EUR][1000 genomes]
rs7551485	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7553916	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs797661	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797666	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs797668	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797671	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797672	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797675	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs797676	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797681	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs942196	0.85[EUR][1000 genomes]
rs9432453	0.86[EUR][1000 genomes]
rs9432465	0.84[EUR][1000 genomes]
rs9432681	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7553465	CCDC18	cis	Nerve Tibial	GTEx
rs7553465	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs7553465	RP4-717I23.3	cis	lung	GTEx
rs7553465	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs7553465	RP4-717I23.3	cis	Artery Tibial	GTEx
rs7553465	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7553465	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs7553465	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs7553465	RP4-717I23.3	cis	Whole Blood	GTEx
rs7553465	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs7553465	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs7553465	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs7553465	RP4-717I23.3	cis	Artery Aorta	GTEx
rs7553465	DR1	cis	multi-tissue	Pritchard
rs7553465	DR1	cis	Adipose Subcutaneous	GTEx
rs7553465	RP4-717I23.3	cis	Thyroid	GTEx
rs7553465	RP4-717I23.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93636200-93644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:93641600-93645000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
7	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:93642400-93645200	Weak transcription	Spleen	Spleen
9	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:93642600-93644600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:93642600-93647800	Active TSS	K562	blood
12	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
13	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:93643000-93644600	Weak transcription	Esophagus	oesophagus
15	chr1:93643000-93644600	Weak transcription	Lung	lung
16	chr1:93643000-93644600	Flanking Active TSS	HUVEC	blood vessel
17	chr1:93643000-93645600	Active TSS	Right Atrium	heart
18	chr1:93643000-93646000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:93643000-93647600	Active TSS	NHLF	lung
21	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
22	chr1:93643200-93644600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:93643200-93644800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:93643200-93646000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
26	chr1:93643200-93647400	Active TSS	A549	lung
27	chr1:93643200-93647600	Active TSS	HMEC	breast
28	chr1:93643400-93644600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:93643400-93644600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:93643400-93644600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:93643400-93644600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr1:93643400-93645200	Active TSS	HepG2	liver
33	chr1:93643400-93645800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:93643400-93646800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:93643400-93646800	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:93643400-93647200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:93643600-93644600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:93643600-93644600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:93643600-93644600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:93643600-93644600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:93643600-93644600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr1:93643600-93644600	Enhancers	Brain Substantia Nigra	brain
43	chr1:93643600-93644600	Flanking Active TSS	Fetal Heart	heart
44	chr1:93643600-93644600	Flanking Active TSS	Fetal Lung	lung
45	chr1:93643600-93644600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:93643600-93644800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:93643600-93644800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr1:93643600-93646600	Active TSS	Ovary	ovary
49	chr1:93643600-93647200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr1:93643600-93647200	Active TSS	H9 Cell Line	embryonic stem cell

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