Variant report

Variant	rs57898225
Chromosome Location	chr1:224700489-224700490
allele	A/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	EGR1	chr1:224700393-224700598	K562	blood:	n/a	chr1:224700501-224700512 chr1:224700503-224700518
2	HNF4A	chr1:224700482-224700784	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:224700377-224700880	HepG2	liver:	n/a	n/a
4	FOXA1	chr1:224700441-224700927	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:224700434-224700861	HepG2	liver:	n/a	n/a
6	SP1	chr1:224700452-224700814	HepG2	liver:	n/a	n/a
7	FOXA1	chr1:224700450-224700823	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224693369..224695979-chr1:224697952..224700518,2	K562	blood:
2	chr1:224700475..224701243-chr1:225038899..225039835,3	MCF-7	breast:

Variant related genes	Relation type
CNIH3	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13376231	1.00[EUR][1000 genomes]
rs55787629	1.00[EUR][1000 genomes]
rs59066189	1.00[EUR][1000 genomes]
rs60544953	1.00[EUR][1000 genomes]
rs60976873	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61004241	1.00[EUR][1000 genomes]
rs61155218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61479600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6676481	1.00[EUR][1000 genomes]
rs6683232	1.00[EUR][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[EUR][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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224690000-224702000	Enhancers	Liver	Liver
2	chr1:224692000-224701600	Weak transcription	Fetal Lung	lung
3	chr1:224692400-224701600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:224692600-224700600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:224694200-224704000	Weak transcription	Right Atrium	heart
6	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224696400-224701200	Weak transcription	Fetal Kidney	kidney
9	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:224697200-224702200	Enhancers	Dnd41	blood
11	chr1:224698200-224700600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:224698600-224700600	Weak transcription	Fetal Intestine Large	intestine
13	chr1:224698600-224701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:224698600-224701200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:224698600-224701400	Weak transcription	Ovary	ovary
16	chr1:224698600-224701400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:224698800-224701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:224698800-224701200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:224698800-224701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:224698800-224701400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:224699000-224700600	Weak transcription	Stomach Mucosa	stomach
22	chr1:224699000-224701400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:224699000-224701600	Weak transcription	NHDF-Ad	bronchial
24	chr1:224699200-224700600	Weak transcription	Fetal Intestine Small	intestine
25	chr1:224699200-224701200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:224699200-224701200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:224699200-224701400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:224699200-224701400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:224699200-224701400	Weak transcription	K562	blood
30	chr1:224699200-224701600	Weak transcription	NH-A	brain
31	chr1:224699200-224701600	Weak transcription	NHEK	skin
32	chr1:224699200-224704200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:224699200-224704600	Weak transcription	HSMM	muscle
34	chr1:224699400-224701200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:224699400-224701200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:224699400-224701200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:224699400-224701600	Weak transcription	HMEC	breast
38	chr1:224699400-224701600	Weak transcription	NHLF	lung
39	chr1:224700000-224701000	Enhancers	HepG2	liver
40	chr1:224700000-224701200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:224700400-224700600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:224700400-224700600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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