Variant report

Variant	rs55738503
Chromosome Location	chr1:93643875-93643876
allele	C/T
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	POLR2A	chr1:93643610-93644056	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:93643705-93644371	K562	blood:	n/a	n/a
3	STAT3	chr1:93643782-93644325	MCF10A-Er-Src	breast:	n/a	n/a
4	JUND	chr1:93643550-93643912	K562	blood:	n/a	n/a
5	POLR2A	chr1:93643852-93644389	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr1:93643872-93644361	Hela-S3	cervix:	n/a	n/a
7	EP300	chr1:93643604-93643923	K562	blood:	n/a	n/a
8	STAT3	chr1:93643871-93644314	MCF10A-Er-Src	breast:	n/a	n/a
9	MXI1	chr1:93643106-93647204	SK-N-SH	brain:	n/a	n/a
10	BHLHE40	chr1:93643717-93644356	K562	blood:	n/a	n/a
11	FOS	chr1:93643536-93643894	HUVEC	blood vessel:	n/a	chr1:93643725-93643736
12	FOSL2	chr1:93643541-93643987	SK-N-SH	brain:	n/a	n/a
13	FOS	chr1:93643574-93643888	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
14	FOS	chr1:93643573-93643921	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
15	MAZ	chr1:93643854-93644681	IMR90	lung:	n/a	n/a
16	FOS	chr1:93643561-93643921	MCF10A-Er-Src	breast:	n/a	chr1:93643725-93643736
17	MYC	chr1:93643589-93644371	MCF10A-Er-Src	breast:	n/a	n/a
18	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	chr1:93543004..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:

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

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10489733	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1057256	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11799543	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11799928	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11800760	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11801175	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11801563	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11802420	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11802421	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11802822	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805267	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807404	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11808445	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12239183	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28829343	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3171	0.82[ASN][1000 genomes]
rs41528947	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55734759	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55741554	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56281837	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56401576	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56657492	1.00[ASN][1000 genomes]
rs58505360	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58770710	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58807475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59368083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59609847	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59774396	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60079850	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60497651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60813039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61252284	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61335636	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61671588	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61690932	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61729705	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6541348	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6541360	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6541398	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6663752	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6664190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6667540	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6671070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677114	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6679304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679630	0.82[ASN][1000 genomes]
rs6688199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6689867	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6695142	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6701683	0.82[ASN][1000 genomes]
rs6704067	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72955402	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72957210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957220	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72957300	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959204	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959216	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959225	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72959236	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959240	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959245	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72959255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959267	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959273	0.82[ASN][1000 genomes]
rs72961310	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72961322	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72961328	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74101458	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74101470	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74104014	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104019	1.00[EUR][1000 genomes]
rs7512471	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7518171	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7518930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7527459	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7529230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533526	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7537939	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7540960	0.82[ASN][1000 genomes]
rs7544352	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7545154	1.00[EUR][1000 genomes]
rs7545358	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7548629	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs754899	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8489	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8561	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9324347	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9662414	0.91[AMR][1000 genomes];0.82[ASN][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

No data

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	chr1:93636200-93644000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:93636200-93644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:93638200-93644000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:93641000-93644000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:93641600-93644000	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr1:93641600-93645000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:93642000-93644000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:93642000-93644200	Enhancers	Small Intestine	intestine
11	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:93642200-93644400	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
14	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:93642400-93645200	Weak transcription	Spleen	Spleen
16	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:93642600-93644600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:93642600-93647800	Active TSS	K562	blood
19	chr1:93642800-93644000	Enhancers	Fetal Muscle Leg	muscle
20	chr1:93642800-93644400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
22	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:93643000-93644600	Weak transcription	Esophagus	oesophagus
24	chr1:93643000-93644600	Weak transcription	Lung	lung
25	chr1:93643000-93644600	Flanking Active TSS	HUVEC	blood vessel
26	chr1:93643000-93645600	Active TSS	Right Atrium	heart
27	chr1:93643000-93646000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:93643000-93647600	Active TSS	NHLF	lung
30	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
31	chr1:93643200-93644000	Genic enhancers	Primary T cells from cord blood	blood
32	chr1:93643200-93644200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:93643200-93644200	Flanking Active TSS	Osteobl	bone
34	chr1:93643200-93644600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:93643200-93644800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:93643200-93646000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
38	chr1:93643200-93647400	Active TSS	A549	lung
39	chr1:93643200-93647600	Active TSS	HMEC	breast
40	chr1:93643400-93644000	Flanking Active TSS	NH-A	brain
41	chr1:93643400-93644200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr1:93643400-93644200	Flanking Active TSS	Liver	Liver
43	chr1:93643400-93644200	Flanking Active TSS	NHEK	skin
44	chr1:93643400-93644400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr1:93643400-93644400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:93643400-93644400	Flanking Active TSS	Fetal Brain Male	brain
47	chr1:93643400-93644400	Enhancers	Gastric	stomach
48	chr1:93643400-93644400	Enhancers	Pancreas	Pancrea
49	chr1:93643400-93644400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:93643400-93644600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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