Variant report

Variant	rs25640
Chromosome Location	chr5:118811533-118811534
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118804681..118808687-chr5:118810812..118814012,4	K562	blood:

Variant related genes	Relation type
ENSG00000239084	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10042168	0.82[CHB][hapmap]
rs10045066	0.82[CHB][hapmap]
rs10051019	0.83[CHB][hapmap]
rs10069875	0.83[CHB][hapmap]
rs10073818	0.81[CHB][hapmap]
rs10078097	0.83[CHB][hapmap]
rs10478426	0.83[CHB][hapmap]
rs11241506	0.81[CHB][hapmap]
rs12653056	0.83[CHB][hapmap]
rs12653702	0.83[CHB][hapmap]
rs13361193	0.83[CHB][hapmap]
rs2075698	0.82[CHB][hapmap]
rs2257900	0.83[ASN][1000 genomes]
rs2259347	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287712	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2303003	0.83[CHB][hapmap]
rs2451816	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2546210	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs257970	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs257971	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257975	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257978	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs26180	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2678070	0.82[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2678091	0.85[ASN][1000 genomes]
rs2945327	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32651	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs32659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32662	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32663	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32665	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35235684	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3797363	0.83[CHB][hapmap]
rs3797367	0.82[CHB][hapmap]
rs3850200	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs455949	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs457106	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs461108	0.86[CHB][hapmap];0.87[GIH][hapmap]
rs463098	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs463513	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs465091	0.91[CHB][hapmap]
rs4895372	0.91[CHB][hapmap]
rs6875595	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs6894991	0.82[CHB][hapmap]
rs6895345	0.82[CHB][hapmap]
rs7721602	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs7721752	0.81[LWK][hapmap]

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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs25640	PRR16	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118789000-118811800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:118789000-118813200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:118789000-118826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:118789200-118813200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:118789400-118831200	Weak transcription	NH-A	brain
6	chr5:118789400-118831600	Weak transcription	HSMMtube	muscle
7	chr5:118789600-118812000	Weak transcription	A549	lung
8	chr5:118789600-118813400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:118789600-118813600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:118789800-118813800	Weak transcription	Fetal Kidney	kidney
11	chr5:118789800-118814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:118790000-118812600	Weak transcription	Fetal Brain Male	brain
13	chr5:118790200-118813400	Weak transcription	Aorta	Aorta
14	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:118792400-118815000	Weak transcription	K562	blood
16	chr5:118793400-118812200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:118794800-118861200	Weak transcription	HSMM	muscle
18	chr5:118795200-118813400	Weak transcription	Small Intestine	intestine
19	chr5:118804200-118813600	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:118804400-118813000	Weak transcription	Colonic Mucosa	Colon
22	chr5:118804400-118813200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:118804400-118820000	Weak transcription	NHDF-Ad	bronchial
24	chr5:118804600-118811800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:118804600-118811800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:118804600-118812000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:118804600-118813400	Weak transcription	Right Ventricle	heart
28	chr5:118804600-118818800	Weak transcription	Stomach Mucosa	stomach
29	chr5:118804600-118819400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:118804800-118811800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:118804800-118813400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:118804800-118821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:118804800-118837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:118805200-118813400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:118805200-118839400	Weak transcription	NHEK	skin
36	chr5:118805400-118812000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:118805400-118812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:118805600-118813000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:118805600-118813400	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:118805600-118817200	Weak transcription	Fetal Brain Female	brain
41	chr5:118805800-118811800	Weak transcription	Primary T cells from cord blood	blood
42	chr5:118805800-118811800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:118805800-118812000	Weak transcription	Adipose Nuclei	Adipose
44	chr5:118805800-118813200	Weak transcription	Fetal Lung	lung
45	chr5:118805800-118817000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:118805800-118829400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:118806000-118811800	Weak transcription	Left Ventricle	heart
48	chr5:118806000-118813400	Weak transcription	Fetal Intestine Small	intestine
49	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
50	chr5:118806000-118846400	Weak transcription	Spleen	Spleen

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