Variant report

Variant	rs7553916
Chromosome Location	chr1:93644843-93644844
allele	C/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	CTCF	chr1:93644809-93644884	GM12892	blood:	n/a	n/a
2	CTCF	chr1:93644840-93644990	HBMEC	blood vessel:	n/a	n/a
3	CEBPB	chr1:93644760-93646220	K562	blood:	n/a	chr1:93645261-93645272
4	CHD1	chr1:93644469-93647061	GM12878	blood:	n/a	chr1:93645456-93645466
5	CTCF	chr1:93644820-93644970	SAEC	small airway:	n/a	n/a
6	ZNF384	chr1:93644782-93645028	K562	blood:	n/a	n/a
7	GATA1	chr1:93644434-93647154	PBDE	blood:	n/a	n/a
8	CTCF	chr1:93644780-93644930	RPTEC	kidney:	n/a	n/a
9	KAP1	chr1:93644498-93646489	HEK293	kidney:	n/a	n/a
10	POLR2A	chr1:93644780-93647219	GM12878	blood:	n/a	n/a
11	MAX	chr1:93644813-93647077	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr1:93644797-93644884	A549	lung:	n/a	n/a
13	CTCF	chr1:93644800-93644950	AG04449	skin:	n/a	n/a
14	CEBPB	chr1:93644804-93646259	K562	blood:	n/a	chr1:93645261-93645272
15	MXI1	chr1:93643106-93647204	SK-N-SH	brain:	n/a	n/a
16	GTF3C2	chr1:93644512-93645392	Hela-S3	cervix:	n/a	n/a
17	SIN3A	chr1:93644717-93647046	GM12878	blood:	n/a	n/a
18	STAT5A	chr1:93644827-93647186	GM12878	blood:	n/a	chr1:93646756-93646768
19	UBTF	chr1:93644774-93644927	K562	blood:	n/a	n/a
20	CEBPB	chr1:93644780-93646653	Hela-S3	cervix:	n/a	chr1:93645261-93645272
21	CTCF	chr1:93644820-93644970	HEEpiC	esophagus:	n/a	n/a
22	CTCF	chr1:93644760-93644910	AG04449	skin:	n/a	n/a
23	CTCF	chr1:93644820-93644970	HCPEpiC	choroid plexus:	n/a	n/a
24	TEAD4	chr1:93644775-93647245	K562	blood:	n/a	n/a
25	CTCF	chr1:93644804-93644886	GM19240	blood:	n/a	n/a
26	NRF1	chr1:93644791-93646627	SK-N-SH	brain:	n/a	chr1:93645463-93645474 chr1:93645463-93645474 chr1:93645463-93645477 chr1:93645460-93645474 chr1:93645465-93645474
27	ZNF384	chr1:93644783-93647140	GM12878	blood:	n/a	n/a
28	CTCF	chr1:93644800-93644950	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr1:93644840-93644990	AG09319	gingival:	n/a	n/a
30	CEBPB	chr1:93644755-93646274	IMR90	lung:	n/a	chr1:93645261-93645272
31	MXI1	chr1:93644776-93647255	IMR90	lung:	n/a	n/a
32	CTCF	chr1:93644760-93644910	GM12869	blood:	n/a	n/a
33	CHD1	chr1:93643454-93647252	IMR90	lung:	n/a	chr1:93645456-93645466

No.	Distal block	Cell Line	Cell type
1	chr1:93643262..93645748-chr1:94311384..94313517,2	K562	blood:
2	chr1:93644741..93645741-chr15:45492796..45493561,2	Hela-S3	cervix:
3	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
4	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
5	chr1:93643769..93645748-chr1:94311324..94312884,2	K562	blood:
6	chr1:93542817..93546420-chr1:93641583..93645468,3	MCF-7	breast:
7	chr1:93644831..93648972-chr1:93800687..93805034,4	K562	blood:
8	chr1:93631724..93634968-chr1:93643710..93645431,3	K562	blood:
9	chr1:93592377..93594266-chr1:93643687..93645200,2	K562	blood:
10	chr1:93296314..93299115-chr1:93644282..93648010,4	K562	blood:
11	chr1:16840807..16843778-chr1:93644585..93646473,2	MCF-7	breast:

Variant related genes	Relation type
CCDC18	TF binding region
ENSG00000143033	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000223745	Chromatin interaction
ENSG00000122406	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000251795	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1057257	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060622	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782955	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782957	0.84[EUR][1000 genomes]
rs10874759	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10874762	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874764	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1088318	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164870	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164871	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164876	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164879	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164880	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164881	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030549	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038699	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12044657	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12118230	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118262	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124011	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124771	0.83[EUR][1000 genomes]
rs12128131	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12130734	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12139009	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12139633	0.86[EUR][1000 genomes]
rs12385720	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1335679	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474927	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1535701	0.83[EUR][1000 genomes]
rs1537758	0.89[ASN][1000 genomes]
rs1572343	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1856027	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1932314	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967721	0.86[ASN][1000 genomes]
rs2152358	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208044	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2295423	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2295424	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296558	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297707	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765545	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783489	0.89[ASN][1000 genomes]
rs35940311	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754184	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3754186	0.83[ASN][1000 genomes]
rs4000699	0.86[EUR][1000 genomes]
rs4847235	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847398	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4847399	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847401	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847402	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs531358	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531514	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs535760	0.83[ASN][1000 genomes]
rs547866	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs555161	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565919	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs602204	0.83[ASN][1000 genomes]
rs612037	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61799471	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs622608	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs624131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627779	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs637646	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6541401	0.82[ASN][1000 genomes]
rs6541404	0.82[ASN][1000 genomes]
rs661126	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6682670	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688230	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682514	0.83[ASN][1000 genomes]
rs687394	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs693737	0.83[ASN][1000 genomes]
rs7418101	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512911	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7513705	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526112	0.80[ASN][1000 genomes]
rs7532195	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7532549	0.81[AMR][1000 genomes]
rs7535628	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539307	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541304	0.80[ASN][1000 genomes]
rs7541687	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551485	0.80[ASN][1000 genomes]
rs7553465	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs797661	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797666	0.83[ASN][1000 genomes]
rs797668	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797671	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs797672	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797675	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs797676	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797681	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9432459	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7553916	RP4-717I23.3	cis	Whole Blood	GTEx
rs7553916	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs7553916	RP4-717I23.3	cis	Thyroid	GTEx
rs7553916	RP4-717I23.3	cis	Artery Aorta	GTEx
rs7553916	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs7553916	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs7553916	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs7553916	RP4-717I23.3	cis	Artery Tibial	GTEx
rs7553916	RP4-717I23.3	cis	lung	GTEx
rs7553916	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7553916	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs7553916	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs7553916	RP4-717I23.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93641600-93645000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
4	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:93642400-93645200	Weak transcription	Spleen	Spleen
6	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:93642600-93647800	Active TSS	K562	blood
8	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
9	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:93643000-93645600	Active TSS	Right Atrium	heart
11	chr1:93643000-93646000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:93643000-93647600	Active TSS	NHLF	lung
14	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
15	chr1:93643200-93646000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
17	chr1:93643200-93647400	Active TSS	A549	lung
18	chr1:93643200-93647600	Active TSS	HMEC	breast
19	chr1:93643400-93645200	Active TSS	HepG2	liver
20	chr1:93643400-93645800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:93643400-93646800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:93643400-93646800	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:93643400-93647200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:93643600-93646600	Active TSS	Ovary	ovary
25	chr1:93643600-93647200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:93643600-93647200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:93643600-93647400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:93643600-93647600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:93643600-93647800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:93643800-93645200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr1:93643800-93645400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:93643800-93646600	Active TSS	Aorta	Aorta
33	chr1:93643800-93646800	Active TSS	Right Ventricle	heart
34	chr1:93643800-93647000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr1:93643800-93647000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr1:93643800-93647200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:93643800-93647200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:93643800-93647200	Active TSS	Colonic Mucosa	Colon
39	chr1:93644000-93645400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:93644000-93646600	Active TSS	Fetal Intestine Small	intestine
41	chr1:93644000-93646800	Active TSS	Brain Angular Gyrus	brain
42	chr1:93644000-93646800	Active TSS	NH-A	brain
43	chr1:93644000-93647800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:93644200-93645000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:93644200-93645000	Weak transcription	Stomach Mucosa	stomach
46	chr1:93644200-93645200	Weak transcription	Small Intestine	intestine
47	chr1:93644200-93645400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:93644200-93645600	Active TSS	Primary T cells fromperipheralblood	blood
49	chr1:93644200-93646400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:93644200-93646600	Active TSS	Fetal Muscle Leg	muscle

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