Variant report

Variant	rs315555
Chromosome Location	chr1:84791239-84791240
allele	A/G
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: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1067072	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1246546	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1246549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1246550	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs160612	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690702	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs1699157	0.92[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17131592	0.87[GIH][hapmap]
rs17131617	0.88[GIH][hapmap]
rs172735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17536473	1.00[CEU][hapmap]
rs178367	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs178368	0.99[ASN][1000 genomes]
rs186405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055115	1.00[CEU][hapmap]
rs315520	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs315521	0.99[ASN][1000 genomes]
rs315522	0.99[ASN][1000 genomes]
rs315523	0.99[ASN][1000 genomes]
rs315524	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs315527	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs315528	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs315531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315532	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315533	0.93[ASN][1000 genomes]
rs315535	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315536	0.99[ASN][1000 genomes]
rs315538	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315539	0.93[ASN][1000 genomes]
rs315540	0.91[ASN][1000 genomes]
rs315546	0.99[ASN][1000 genomes]
rs315547	0.92[ASN][1000 genomes]
rs315548	0.99[ASN][1000 genomes]
rs315549	0.99[ASN][1000 genomes]
rs315552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315553	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs315554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316644	0.81[CHD][hapmap]
rs316660	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs316661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs316662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs316664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316665	1.00[ASN][1000 genomes]
rs511087	0.99[ASN][1000 genomes]
rs592464	1.00[ASN][1000 genomes]
rs786653	0.92[EUR][1000 genomes];0.92[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs315555	HIVEP2	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84769200-84791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:84780200-84791400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:84785800-84797800	Weak transcription	Gastric	stomach
4	chr1:84786600-84801600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:84787600-84793800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:84787600-84796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:84789000-84791600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:84789000-84795200	Weak transcription	Aorta	Aorta
9	chr1:84789600-84791400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:84789600-84795400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:84789800-84791800	Weak transcription	Colonic Mucosa	Colon
12	chr1:84789800-84797200	Weak transcription	Fetal Stomach	stomach
13	chr1:84790000-84793200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:84790200-84795400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:84790600-84792800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:84790600-84795800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:84790800-84791600	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr1:84790800-84796400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:84791000-84791400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:84791200-84791600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr1:84791200-84791800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:84791200-84792400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:84791200-84792800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:84791200-84793000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:84791200-84793200	Strong transcription	Brain Hippocampus Middle	brain
26	chr1:84791200-84794800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:84791200-84794800	Weak transcription	Pancreas	Pancrea
28	chr1:84791200-84795800	Strong transcription	Rectal Mucosa Donor 29	rectum

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