Variant report

Variant	rs315553
Chromosome Location	chr1:84792973-84792974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84764306..84766033-chr1:84791086..84793194,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203943	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1067072	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1246546	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1246549	0.90[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1246550	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs160612	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1690702	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1699157	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17131613	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17131617	1.00[CEU][hapmap]
rs17131618	1.00[CEU][hapmap]
rs172735	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs178367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178368	0.92[ASN][1000 genomes]
rs186405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs315520	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315521	0.92[ASN][1000 genomes]
rs315522	0.92[ASN][1000 genomes]
rs315523	0.92[ASN][1000 genomes]
rs315524	0.92[ASN][1000 genomes]
rs315525	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs315526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315527	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs315528	0.94[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs315530	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs315531	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs315532	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs315533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315535	0.99[ASN][1000 genomes]
rs315536	0.92[ASN][1000 genomes]
rs315538	0.92[ASN][1000 genomes]
rs315539	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315540	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315546	0.92[ASN][1000 genomes]
rs315547	0.99[ASN][1000 genomes]
rs315548	0.92[ASN][1000 genomes]
rs315549	0.92[ASN][1000 genomes]
rs315552	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs315554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs315555	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs315556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs316660	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316661	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs316663	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs316665	0.93[ASN][1000 genomes]
rs511087	0.92[ASN][1000 genomes]
rs592464	0.93[ASN][1000 genomes]
rs786653	0.99[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	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84785800-84797800	Weak transcription	Gastric	stomach
2	chr1:84786600-84801600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:84787600-84793800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:84787600-84796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:84789000-84795200	Weak transcription	Aorta	Aorta
6	chr1:84789600-84795400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:84789800-84797200	Weak transcription	Fetal Stomach	stomach
8	chr1:84790000-84793200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:84790200-84795400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:84790600-84795800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr1:84790800-84796400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:84791200-84793000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:84791200-84793200	Strong transcription	Brain Hippocampus Middle	brain
14	chr1:84791200-84794800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:84791200-84794800	Weak transcription	Pancreas	Pancrea
16	chr1:84791200-84795800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:84791400-84793000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:84791600-84793200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:84791600-84794600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:84791800-84793600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:84792000-84794000	Weak transcription	Colonic Mucosa	Colon
22	chr1:84792200-84795200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:84792200-84795600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:84792200-84797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:84792400-84793200	Enhancers	Fetal Intestine Small	intestine
26	chr1:84792400-84795400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:84792400-84795800	Weak transcription	Primary T cells from cord blood	blood
28	chr1:84792400-84797200	Weak transcription	Fetal Intestine Large	intestine
29	chr1:84792800-84793200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:84792800-84795000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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