Variant report

Variant	rs60544953
Chromosome Location	chr1:224701988-224701989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:224701145-224702120	HCT-116	colon:	n/a	n/a
2	GATA3	chr1:224701881-224702097	SH-SY5Y	brain:	n/a	n/a
3	CTCF	chr1:224701350-224702000	IMR90	lung:	n/a	n/a
4	SMC3	chr1:224701322-224702000	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr1:224701170-224702235	A549	lung:	n/a	n/a
6	SMC3	chr1:224701160-224702163	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr1:224701185-224702176	HCT-116	colon:	n/a	n/a
8	CTCF	chr1:224701105-224702180	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr1:224701200-224702091	HCT-116	colon:	n/a	n/a
10	RAD21	chr1:224701171-224702029	HCT-116	colon:	n/a	n/a
11	RAD21	chr1:224701079-224702250	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr1:224701236-224701988	A549	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224701549..224702083-chr1:225038942..225039865,2	MCF-7	breast:
2	chr1:224701543..224702095-chr1:224768528..224769263,2	K562	blood:

No data

Variant related genes	Relation type
CNIH3	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13376231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376387	1.00[AFR][1000 genomes]
rs55712053	1.00[AMR][1000 genomes]
rs55787629	1.00[EUR][1000 genomes]
rs57898225	1.00[EUR][1000 genomes]
rs59066189	1.00[EUR][1000 genomes]
rs60976873	1.00[EUR][1000 genomes]
rs61004241	1.00[EUR][1000 genomes]
rs61155217	1.00[AMR][1000 genomes]
rs61155218	1.00[EUR][1000 genomes]
rs61479600	1.00[EUR][1000 genomes]
rs6659109	1.00[AMR][1000 genomes]
rs6676481	1.00[EUR][1000 genomes]
rs6683232	1.00[EUR][1000 genomes]
rs6687424	1.00[AMR][1000 genomes]
rs74146364	1.00[EUR][1000 genomes]
rs74146365	1.00[EUR][1000 genomes]
rs74146366	1.00[EUR][1000 genomes]
rs74146367	1.00[EUR][1000 genomes]
rs74146368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74146372	1.00[AMR][1000 genomes]
rs74146374	1.00[AMR][1000 genomes]
rs7522430	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224690000-224702000	Enhancers	Liver	Liver
2	chr1:224694200-224704000	Weak transcription	Right Atrium	heart
3	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:224697200-224702200	Enhancers	Dnd41	blood
7	chr1:224699200-224704200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224699200-224704600	Weak transcription	HSMM	muscle
9	chr1:224701200-224702000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:224701200-224702000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:224701200-224702000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:224701200-224702000	Enhancers	Fetal Brain Male	brain
13	chr1:224701200-224702000	Enhancers	Fetal Kidney	kidney
14	chr1:224701200-224703200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:224701400-224702000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:224701400-224702000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:224701400-224702000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:224701400-224702000	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:224701400-224702000	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:224701400-224702000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:224701400-224704200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:224701600-224702000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:224701600-224702000	Enhancers	Fetal Lung	lung
24	chr1:224701600-224702000	Enhancers	NH-A	brain
25	chr1:224701600-224702000	Enhancers	NHDF-Ad	bronchial
26	chr1:224701600-224702000	Enhancers	NHLF	lung
27	chr1:224701800-224703000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:224701800-224704000	Weak transcription	K562	blood
29	chr1:224701800-224705400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:224701800-224709200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:224701800-224716600	Weak transcription	Ovary	ovary

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