Variant report

Variant	rs41292683
Chromosome Location	chr1:94527088-94527089
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	CTCF	chr1:94527080-94527230	GM12866	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
2	GTF2F1	chr1:94527054-94527376	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:94527014-94527334	GM19238	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
4	CTCF	chr1:94526516-94527745	SK-N-SH	brain:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
5	RAD21	chr1:94526935-94527408	H1-hESC	embryonic stem cell:	n/a	chr1:94527158-94527177
6	CTCF	chr1:94527060-94527210	BE2_C	brain:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
7	CTCF	chr1:94527029-94527320	A549	lung:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
8	CTCF	chr1:94527037-94527290	MCF-7	breast:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
9	CTCF	chr1:94526929-94527398	K562	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
10	CTCF	chr1:94527060-94527210	GM12871	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
11	CTCF	chr1:94527080-94527230	GM06990	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
12	CTCF	chr1:94527040-94527190	HFF	foreskin:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
13	RAD21	chr1:94526965-94527446	MCF-7	breast:	n/a	chr1:94527158-94527177
14	CTCF	chr1:94527080-94527230	BE2_C	brain:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
15	TBL1XR1	chr1:94527015-94527317	GM12878	blood:	n/a	n/a
16	CTCF	chr1:94527080-94527230	GM12871	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
17	CTCF	chr1:94527060-94527210	HUVEC	blood vessel:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
18	CTCF	chr1:94527060-94527210	GM12868	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
19	RAD21	chr1:94526947-94527400	Hela-S3	cervix:	n/a	chr1:94527158-94527177
20	SMC3	chr1:94526443-94528709	SK-N-SH	brain:	n/a	chr1:94527159-94527166 chr1:94527159-94527173
21	CTCF	chr1:94527033-94527299	ProgFib	skin:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
22	ZNF143	chr1:94526984-94527355	GM12878	blood:	n/a	n/a
23	CTCF	chr1:94527016-94527318	Gliobla	brain:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
24	FOXP2	chr1:94527023-94527277	SK-N-MC	brain:	n/a	n/a
25	CTCF	chr1:94527047-94527304	MCF-7	breast:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
26	CTCF	chr1:94526990-94527364	K562	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
27	MAX	chr1:94527002-94527231	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:94527059-94527306	MCF-7	breast:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
29	CTCF	chr1:94527067-94527258	A549	lung:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
30	CTCF	chr1:94527023-94527308	MCF-7	breast:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
31	RAD21	chr1:94526763-94527535	A549	lung:	n/a	chr1:94527158-94527177
32	RAD21	chr1:94526781-94528114	HCT-116	colon:	n/a	chr1:94527158-94527177
33	CTCF	chr1:94527011-94527295	LNCaP	prostate:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
34	CTCF	chr1:94526749-94527791	HCT-116	colon:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
35	CTCF	chr1:94527045-94527299	MCF-7	breast:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
36	CTCF	chr1:94526937-94527309	HepG2	liver:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
37	CTCF	chr1:94527060-94527210	GM12878	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
38	CTCF	chr1:94526980-94527130	HAc	cerebellar:	n/a	n/a
39	CTCF	chr1:94527060-94527210	RPTEC	kidney:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
40	SP4	chr1:94526942-94527320	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr1:94527024-94527345	SK-N-SH_RA	brain:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
42	CTCF	chr1:94527040-94527190	NHLF	lung:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
43	RAD21	chr1:94526967-94527463	MCF-7	breast:	n/a	chr1:94527158-94527177
44	CTCF	chr1:94527000-94527150	A549	lung:	n/a	n/a
45	CTCF	chr1:94527080-94527230	HPF	lung:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
46	CTCF	chr1:94527022-94527319	GM19240	blood:	n/a	chr1:94527157-94527175 chr1:94527160-94527169 chr1:94527159-94527180
47	FOXM1	chr1:94526926-94527368	GM12878	blood:	n/a	n/a
48	RAD21	chr1:94526974-94527976	HepG2	liver:	n/a	chr1:94527158-94527177
49	BRCA1	chr1:94527009-94527289	Hela-S3	cervix:	n/a	n/a
50	YY1	chr1:94526964-94527341	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94527081..94529532-chr1:94702506..94704195,2	MCF-7	breast:
2	chr1:94527064..94527740-chr1:94706101..94706691,3	MCF-7	breast:
3	chr1:94524835..94527724-chr1:94798552..94800345,2	MCF-7	breast:
4	chr1:94526735..94527649-chr1:94702636..94703585,3	MCF-7	breast:

Variant related genes	Relation type
ABCA4	TF binding region
ENSG00000226835	Chromatin interaction
ENSG00000137962	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17392507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801581	0.83[EUR][1000 genomes]
rs4147835	1.00[EUR][1000 genomes]
rs55712710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56197337	1.00[EUR][1000 genomes]
rs56375042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658767	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72725166	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72725167	1.00[EUR][1000 genomes]
rs72725169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72725178	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72725182	1.00[AMR][1000 genomes];0.87[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	nsv871172	chr1:94504545-94535546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv871057	chr1:94513142-94577286	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94515800-94527200	Weak transcription	Spleen	Spleen
2	chr1:94517200-94527200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:94521000-94534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:94521400-94527200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:94522000-94527200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:94522200-94527200	Weak transcription	NHEK	skin
7	chr1:94522200-94533800	Weak transcription	Aorta	Aorta
8	chr1:94522400-94527200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:94522600-94528600	Weak transcription	Fetal Lung	lung
10	chr1:94522600-94533200	Weak transcription	Gastric	stomach
11	chr1:94522800-94533400	Weak transcription	Stomach Mucosa	stomach
12	chr1:94523200-94533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:94523600-94530400	Enhancers	Left Ventricle	heart
14	chr1:94523800-94527200	Weak transcription	Psoas Muscle	Psoas
15	chr1:94524200-94527600	Weak transcription	Lung	lung
16	chr1:94524400-94527800	Enhancers	Right Atrium	heart
17	chr1:94524600-94531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:94525000-94530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:94525200-94527200	Weak transcription	Right Ventricle	heart
20	chr1:94525200-94529600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:94525400-94527200	Enhancers	HepG2	liver
22	chr1:94525800-94529000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:94526000-94527200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:94526000-94530200	Enhancers	HUVEC	blood vessel
25	chr1:94526000-94530400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:94526200-94533600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:94526600-94527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:94526600-94527200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:94526600-94527400	Enhancers	Fetal Muscle Leg	muscle
30	chr1:94526600-94528200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:94526600-94528200	Enhancers	Adipose Nuclei	Adipose
32	chr1:94526600-94530200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:94526800-94527200	Enhancers	A549	lung
34	chr1:94526800-94527400	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:94526800-94527400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:94526800-94527600	Enhancers	Stomach Smooth Muscle	stomach
37	chr1:94526800-94527800	Enhancers	Pancreas	Pancrea
38	chr1:94526800-94527800	Enhancers	HSMMtube	muscle
39	chr1:94526800-94528000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:94526800-94528000	Enhancers	HMEC	breast
41	chr1:94526800-94528200	Enhancers	Liver	Liver
42	chr1:94526800-94529000	Enhancers	HSMM	muscle
43	chr1:94526800-94530200	Enhancers	NHDF-Ad	bronchial
44	chr1:94527000-94527400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:94527000-94527400	Enhancers	Hela-S3	cervix
46	chr1:94527000-94527600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:94527000-94527600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:94527000-94527800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:94527000-94528600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:94527000-94529400	Enhancers	NH-A	brain

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