Variant report

Variant	rs10799563
Chromosome Location	chr1:224516844-224516845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224515424..224519366-chr1:224544067..224546170,3	K562	blood:
2	chr1:223899719..223902673-chr1:224516675..224518721,2	K562	blood:
3	chr1:224514132..224518075-chr1:224542843..224545822,3	K562	blood:
4	chr1:224516510..224520785-chr1:224542312..224545237,4	MCF-7	breast:
5	chr1:224299141..224303224-chr1:224514971..224520507,6	MCF-7	breast:
6	chr1:224301491..224304269-chr1:224515082..224517266,2	K562	blood:
7	chr1:224301216..224303713-chr1:224515346..224517425,2	K562	blood:
8	chr1:224301568..224304233-chr1:224516678..224521021,7	MCF-7	breast:
9	chr1:224509313..224513454-chr1:224513971..224516940,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10158063	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10733024	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737442	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737443	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753462	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753464	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799562	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799566	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799567	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799568	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916577	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916585	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802486	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11811730	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846031	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846094	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846214	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846244	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806742	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001712	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001713	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2404783	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404856	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404857	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404859	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404861	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405062	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405065	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405067	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405070	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2896990	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897054	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754090	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767721	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767722	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767724	1.00[ASN][1000 genomes]
rs3767725	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146965	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146966	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233234	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256779	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4420060	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457542	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4628473	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653575	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653581	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653583	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653584	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654011	0.88[ASN][1000 genomes]
rs4654017	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654019	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654022	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654023	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654032	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654033	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654034	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55675086	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55980628	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57324770	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58855990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59106681	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426088	0.91[ASN][1000 genomes]
rs6426094	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426100	0.81[ASN][1000 genomes]
rs6426110	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426114	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6426115	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426117	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681790	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682667	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685600	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6691689	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694745	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696795	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699017	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118046	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73128468	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130436	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130448	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130455	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130462	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130464	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521015	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522392	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7529143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530205	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534101	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534447	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287027	1.00[EUR][1000 genomes];0.91[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224482800-224517000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:224483800-224517200	Weak transcription	Small Intestine	intestine
3	chr1:224496000-224517000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:224498000-224517000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:224498000-224517200	Weak transcription	Aorta	Aorta
6	chr1:224504200-224517000	Weak transcription	HSMMtube	muscle
7	chr1:224504400-224517200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:224504400-224517200	Weak transcription	Pancreas	Pancrea
9	chr1:224504400-224517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:224510000-224517400	Weak transcription	Spleen	Spleen
11	chr1:224513600-224517200	Weak transcription	Lung	lung
12	chr1:224513800-224517200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:224514200-224517000	Enhancers	Liver	Liver
14	chr1:224514400-224517000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:224514800-224517000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:224515000-224517400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:224515400-224517000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:224515400-224517000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:224515400-224517000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:224515600-224517200	Weak transcription	Stomach Mucosa	stomach
21	chr1:224516000-224517000	Enhancers	Primary B cells from cord blood	blood
22	chr1:224516000-224517000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:224516000-224517000	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:224516000-224517000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:224516200-224517000	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:224516200-224517000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:224516200-224517000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:224516200-224517000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:224516200-224517000	Enhancers	Fetal Heart	heart
30	chr1:224516200-224517000	Enhancers	Fetal Lung	lung
31	chr1:224516200-224517200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:224516200-224517200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:224516200-224517200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:224516200-224517200	Flanking Active TSS	Dnd41	blood
35	chr1:224516200-224518600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:224516200-224518800	Active TSS	H1 Cell Line	embryonic stem cell
37	chr1:224516200-224518800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:224516200-224518800	Active TSS	Fetal Kidney	kidney
39	chr1:224516200-224518800	Active TSS	NHDF-Ad	bronchial
40	chr1:224516400-224517000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr1:224516400-224517000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:224516400-224517000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:224516400-224517000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:224516400-224517000	Enhancers	Brain Anterior Caudate	brain
45	chr1:224516400-224517000	Enhancers	Brain Hippocampus Middle	brain
46	chr1:224516400-224517000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:224516400-224517000	Weak transcription	Brain Substantia Nigra	brain
48	chr1:224516400-224517000	Enhancers	Colonic Mucosa	Colon
49	chr1:224516400-224517000	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr1:224516400-224517000	Enhancers	Placenta Amnion	Placenta Amnion

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