Variant report

Variant	rs17131825
Chromosome Location	chr7:47854667-47854668
allele	C/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	RAD21	chr7:47854515-47854908	H1-hESC	embryonic stem cell:	n/a	n/a
2	NR3C1	chr7:47854567-47854904	A549	lung:	n/a	chr7:47854766-47854780 chr7:47854764-47854781 chr7:47854721-47854728
3	NR3C1	chr7:47854537-47854925	A549	lung:	n/a	chr7:47854766-47854780 chr7:47854764-47854781 chr7:47854721-47854728
4	NFIC	chr7:47854450-47855226	ECC-1	luminal epithelium:	n/a	n/a
5	NR3C1	chr7:47854498-47855051	A549	lung:	n/a	chr7:47854766-47854780 chr7:47854764-47854781 chr7:47854721-47854728
6	NR3C1	chr7:47854546-47854932	A549	lung:	n/a	chr7:47854766-47854780 chr7:47854764-47854781 chr7:47854721-47854728
7	TEAD4	chr7:47854411-47854978	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr7:47854502-47854903	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr7:47854578-47854906	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr7:47854453-47854990	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47847893..47850671-chr7:47853007..47855421,2	K562	blood:

Variant related genes	Relation type
PKD1L1	TF binding region
ENSG00000158683	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10429127	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12702392	0.82[EUR][1000 genomes]
rs12702393	0.80[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12702395	1.00[JPT][hapmap]
rs13231277	0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs13239205	0.81[EUR][1000 genomes]
rs13241400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247692	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13247756	0.92[EUR][1000 genomes]
rs17131827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17131855	0.92[EUR][1000 genomes]
rs17545682	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1851403	0.91[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs2053985	0.81[MEX][hapmap]
rs2123610	0.92[EUR][1000 genomes]
rs34069037	0.94[EUR][1000 genomes]
rs34703899	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34712849	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35030912	0.81[EUR][1000 genomes]
rs35781192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4391316	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66733202	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66755489	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67572268	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6947342	1.00[JPT][hapmap]
rs6950328	0.91[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6962855	1.00[JPT][hapmap]
rs6970132	0.81[EUR][1000 genomes]
rs73103467	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7788583	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs7802098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17131825	TMED4	cis	parietal	SCAN
rs17131825	UPP1	cis	cerebellum	SCAN
rs17131825	SNORA5C	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47846800-47858600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:47847600-47855800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:47847600-47858800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:47848400-47857600	Weak transcription	HSMMtube	muscle
5	chr7:47851200-47854800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr7:47851200-47855200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr7:47852400-47857800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:47852800-47855600	Weak transcription	Right Ventricle	heart
9	chr7:47852800-47856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:47853000-47855800	Enhancers	Adipose Nuclei	Adipose
12	chr7:47853000-47858600	Weak transcription	Placenta	Placenta
13	chr7:47853400-47858800	Weak transcription	Brain Substantia Nigra	brain
14	chr7:47853400-47859800	Enhancers	A549	lung
15	chr7:47853600-47855000	Weak transcription	HepG2	liver
16	chr7:47853600-47855200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:47853600-47858600	Weak transcription	Fetal Intestine Large	intestine
18	chr7:47853800-47854800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr7:47853800-47858800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:47854000-47855000	Enhancers	Lung	lung
21	chr7:47854000-47855200	Enhancers	Left Ventricle	heart
22	chr7:47854000-47858600	Weak transcription	Fetal Intestine Small	intestine
23	chr7:47854200-47855000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:47854200-47855600	Weak transcription	Spleen	Spleen
25	chr7:47854400-47855000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr7:47854400-47855000	Enhancers	Fetal Heart	heart
27	chr7:47854600-47854800	Enhancers	Brain Anterior Caudate	brain
28	chr7:47854600-47854800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:47854600-47854800	Enhancers	Fetal Muscle Leg	muscle
30	chr7:47854600-47855000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:47854600-47855000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr7:47854600-47855000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr7:47854600-47855000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:47854600-47855000	Enhancers	Fetal Muscle Trunk	muscle
35	chr7:47854600-47855400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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