Variant report

Variant	rs35779894
Chromosome Location	chr1:184727100-184727101
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	FOXA1	chr1:184727067-184727380	T-47D	breast:	n/a	chr1:184727274-184727289

No.	Distal block	Cell Line	Cell type
1	chr1:184726814..184728500-chr1:184735928..184737770,2	K562	blood:
2	chr1:184722577..184724889-chr1:184727067..184730117,4	MCF-7	breast:
3	chr1:184725745..184728657-chr1:184756568..184759148,2	MCF-7	breast:

Variant related genes	Relation type
EDEM3	TF binding region
ENSG00000116406	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489697	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10911637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]
rs12060621	0.81[AFR][1000 genomes]
rs12067111	0.95[AFR][1000 genomes]
rs12079454	1.00[ASN][1000 genomes]
rs12094196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes]
rs12096214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs16823413	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16823421	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16823429	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2224092	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41535944	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs489435	1.00[JPT][hapmap]
rs538337	1.00[JPT][hapmap]
rs55896922	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56384325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56741490	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs569243	1.00[JPT][hapmap]
rs58465130	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs59085958	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59347366	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59862212	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs603160	1.00[JPT][hapmap]
rs61022402	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823879	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61823880	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823882	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823885	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823891	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61823908	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs641658	1.00[JPT][hapmap]
rs642027	1.00[JPT][hapmap]
rs6681178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861578	0.81[YRI][hapmap]
rs861581	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184724600-184728800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:184724800-184742600	Weak transcription	Gastric	stomach
3	chr1:184725000-184728400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:184725200-184727200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:184725200-184728600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:184725200-184728800	Weak transcription	HSMMtube	muscle
7	chr1:184725200-184731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:184725400-184730000	Enhancers	Stomach Mucosa	stomach
9	chr1:184725600-184728200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:184725600-184728400	Weak transcription	A549	lung
11	chr1:184725600-184728600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:184725800-184727800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:184725800-184728000	Weak transcription	HepG2	liver
14	chr1:184725800-184728400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:184726600-184728800	Enhancers	Liver	Liver
16	chr1:184727000-184729000	Weak transcription	Pancreas	Pancrea

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