Variant report

Variant	rs17545564
Chromosome Location	chr7:47854956-47854957
allele	C/T
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	NFIC	chr7:47854450-47855226	ECC-1	luminal epithelium:	n/a	n/a
2	NR3C1	chr7:47854498-47855051	A549	lung:	n/a	chr7:47854766-47854780 chr7:47854764-47854781 chr7:47854721-47854728
3	TEAD4	chr7:47854411-47854978	ECC-1	luminal epithelium:	n/a	n/a
4	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: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11765736	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11769398	0.86[JPT][hapmap]
rs12668946	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs12673502	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs17627961	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659868	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs17710874	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17710880	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs2123609	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs2290386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348460	0.91[JPT][hapmap]
rs2348462	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4724648	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4724650	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6959021	0.89[CEU][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs73692834	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639988	0.88[CEU][hapmap];0.80[AMR][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

No data

Chromatin state (count:33 , 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	chr7:47851200-47855200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:47852400-47857800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:47852800-47855600	Weak transcription	Right Ventricle	heart
8	chr7:47852800-47856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:47853000-47855800	Enhancers	Adipose Nuclei	Adipose
11	chr7:47853000-47858600	Weak transcription	Placenta	Placenta
12	chr7:47853400-47858800	Weak transcription	Brain Substantia Nigra	brain
13	chr7:47853400-47859800	Enhancers	A549	lung
14	chr7:47853600-47855000	Weak transcription	HepG2	liver
15	chr7:47853600-47855200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:47853600-47858600	Weak transcription	Fetal Intestine Large	intestine
17	chr7:47853800-47858800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:47854000-47855000	Enhancers	Lung	lung
19	chr7:47854000-47855200	Enhancers	Left Ventricle	heart
20	chr7:47854000-47858600	Weak transcription	Fetal Intestine Small	intestine
21	chr7:47854200-47855000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:47854200-47855600	Weak transcription	Spleen	Spleen
23	chr7:47854400-47855000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr7:47854400-47855000	Enhancers	Fetal Heart	heart
25	chr7:47854600-47855000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:47854600-47855000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr7:47854600-47855000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr7:47854600-47855000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:47854600-47855000	Enhancers	Fetal Muscle Trunk	muscle
30	chr7:47854600-47855400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr7:47854800-47855200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr7:47854800-47856000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:47854800-47858600	Weak transcription	Fetal Muscle Leg	muscle

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