Variant report

Variant	rs4774273
Chromosome Location	chr15:57889729-57889730
allele	A/C
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	NR2F2	chr15:57889678-57890240	MCF-7	breast:	n/a	n/a
2	NR2F2	chr15:57889704-57890228	MCF-7	breast:	n/a	n/a
3	GATA3	chr15:57889714-57890259	MCF-7	breast:	n/a	chr15:57889714-57889723

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57884863..57887415-chr15:57888908..57890684,2	MCF-7	breast:

Variant related genes	Relation type
MYZAP	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152878	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851618	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071335	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852838	1.00[ASN][1000 genomes]
rs11853270	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11856824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12323998	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324010	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12324289	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12442978	1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12442987	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs12443389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380406	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380418	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346125	1.00[ASN][1000 genomes]
rs16977630	1.00[CHB][hapmap]
rs17239937	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172608	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557258	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4774282	1.00[ASN][1000 genomes]
rs4774971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774974	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57589057	1.00[ASN][1000 genomes]
rs58017146	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58919063	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61600143	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178159	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743512	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743516	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745565	1.00[ASN][1000 genomes]
rs7359330	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs74016366	1.00[ASN][1000 genomes]
rs9796502	0.91[CEU][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking 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	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	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
rs4774273	PAPD7	trans	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57885200-57891600	Enhancers	Fetal Intestine Large	intestine
2	chr15:57885200-57899000	Weak transcription	Hela-S3	cervix
3	chr15:57885200-57899400	Weak transcription	HUVEC	blood vessel
4	chr15:57885200-57899800	Weak transcription	Placenta	Placenta
5	chr15:57885400-57891000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:57885400-57894600	Enhancers	Pancreas	Pancrea
7	chr15:57885600-57891400	Enhancers	Stomach Mucosa	stomach
8	chr15:57885800-57889800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:57886000-57892000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:57886600-57890000	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr15:57886600-57896600	Enhancers	Adipose Nuclei	Adipose
12	chr15:57886800-57891600	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:57886800-57891800	Enhancers	Colon Smooth Muscle	Colon
14	chr15:57887000-57890400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:57887200-57890000	Enhancers	Ovary	ovary
16	chr15:57887200-57891000	Enhancers	Right Atrium	heart
17	chr15:57887800-57899200	Weak transcription	Colonic Mucosa	Colon
18	chr15:57887800-57899200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:57888000-57890600	Enhancers	Spleen	Spleen
20	chr15:57888000-57891000	Enhancers	Right Ventricle	heart
21	chr15:57888200-57890800	Weak transcription	Psoas Muscle	Psoas
22	chr15:57888200-57890800	Weak transcription	Small Intestine	intestine
23	chr15:57888200-57891600	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:57888400-57889800	Enhancers	Gastric	stomach
25	chr15:57888600-57893800	Weak transcription	Thymus	Thymus
26	chr15:57888800-57889800	Genic enhancers	Fetal Intestine Small	intestine
27	chr15:57888800-57890000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:57888800-57890000	Enhancers	HMEC	breast
29	chr15:57888800-57890200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:57888800-57890200	Enhancers	Lung	lung
31	chr15:57889000-57890000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:57889000-57890000	Enhancers	NHEK	skin
33	chr15:57889000-57891600	Enhancers	Left Ventricle	heart
34	chr15:57889600-57889800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:57889600-57889800	Enhancers	Rectal Smooth Muscle	rectum
36	chr15:57889600-57889800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr15:57889600-57890000	Flanking Active TSS	Esophagus	oesophagus
38	chr15:57889600-57890000	Enhancers	Fetal Heart	heart
39	chr15:57889600-57890200	Enhancers	Fetal Lung	lung
40	chr15:57889600-57890200	Enhancers	Fetal Stomach	stomach
41	chr15:57889600-57892600	Enhancers	Rectal Mucosa Donor 31	rectum

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