Variant report

Variant	rs10799505
Chromosome Location	chr1:224351023-224351024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224350776..224352461-chr1:224370770..224373033,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10753454	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799478	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799480	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916301	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916307	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916320	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916355	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916367	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916403	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916415	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11808787	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12038372	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049583	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12070670	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12076788	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12563153	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730611	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13374070	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492694	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844819	0.89[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17560970	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1826421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2011117	0.81[CHB][hapmap];0.81[MEX][hapmap]
rs2014782	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048997	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051105	0.90[ASN][1000 genomes]
rs2172361	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280291	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404843	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2896985	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767730	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820482	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820483	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653563	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653568	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4653972	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653991	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653994	0.87[ASN][1000 genomes]
rs4653995	0.85[ASN][1000 genomes]
rs4654003	0.81[CHB][hapmap]
rs55664906	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55736782	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61827699	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426139	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426143	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426169	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426178	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs66506223	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657467	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658494	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659234	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680651	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681673	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6682292	0.81[CHB][hapmap]
rs6682551	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685405	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688818	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690695	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698041	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6700284	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7511895	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7518839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524705	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542293	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546235	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869945	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs908795	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs908801	0.81[CHB][hapmap]
rs997296	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1792939	chr1:224336636-224351023	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10799505	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs10799505	KIAA0483	cis	multi-tissue	Pritchard
rs10799505	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10799505	BPNT1	cis	parietal	SCAN
rs10799505	FBXO28	cis	lymphoblastoid	seeQTL
rs10799505	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:224327600-224356400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:224339200-224363200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:224345400-224351400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224345400-224352200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:224345400-224363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:224345600-224351400	Weak transcription	Gastric	stomach
9	chr1:224345600-224352000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:224345600-224363400	Weak transcription	Ovary	ovary
11	chr1:224345800-224356600	Weak transcription	Small Intestine	intestine
12	chr1:224346000-224351400	Weak transcription	Fetal Heart	heart
13	chr1:224346000-224356600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:224346200-224356000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:224346200-224356600	Weak transcription	NHLF	lung
16	chr1:224346400-224356600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
18	chr1:224346600-224356400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:224346600-224356400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:224346600-224356400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:224346600-224356600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:224346600-224356600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:224346600-224356600	Weak transcription	Aorta	Aorta
24	chr1:224346600-224356600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:224346600-224356600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:224346600-224356600	Weak transcription	Thymus	Thymus
27	chr1:224346600-224356600	Weak transcription	HSMMtube	muscle
28	chr1:224346600-224358200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:224346600-224363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:224346600-224363200	Weak transcription	Fetal Stomach	stomach
31	chr1:224346600-224363400	Weak transcription	Right Ventricle	heart
32	chr1:224346600-224363400	Weak transcription	Spleen	Spleen
33	chr1:224346800-224351200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:224346800-224352200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:224346800-224356400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:224346800-224356400	Weak transcription	NHEK	skin
37	chr1:224346800-224356600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:224346800-224356600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:224346800-224356600	Weak transcription	Psoas Muscle	Psoas
40	chr1:224347000-224351400	Weak transcription	Fetal Brain Female	brain
41	chr1:224347000-224352400	Weak transcription	Brain Germinal Matrix	brain
42	chr1:224347000-224356200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:224347200-224356400	Weak transcription	HepG2	liver
44	chr1:224347200-224356600	Weak transcription	GM12878-XiMat	blood
45	chr1:224347400-224351800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:224347400-224356000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:224347600-224356000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:224347600-224356400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:224347600-224356400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:224348000-224356600	Weak transcription	HMEC	breast

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