Variant report

Variant	rs2483679
Chromosome Location	chr1:10485019-10485020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10746494	0.84[ASN][1000 genomes]
rs11121579	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12565133	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1307485	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1307487	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1750349	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1760664	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2483684	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2781233	0.82[JPT][hapmap]
rs475549	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481571	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491880	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505141	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517241	0.98[ASN][1000 genomes]
rs519472	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520964	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522029	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522280	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs524150	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs528713	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs579398	0.94[ASN][1000 genomes]
rs583515	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585703	0.97[ASN][1000 genomes]
rs586096	0.80[ASN][1000 genomes]
rs586223	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597441	0.80[MEX][hapmap]
rs628462	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs632690	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634358	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649101	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649639	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666583	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667366	0.94[ASN][1000 genomes]
rs670666	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs678850	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs681448	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681495	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv3319265	chr1:10480465-10485563	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2483679	KIF1B	cis	multi-tissue	Pritchard
rs2483679	SLC2A5	cis	cerebellum	SCAN
rs2483679	APITD1	cis	cerebellum	SCAN
rs2483679	KIAA2013	cis	parietal	SCAN
rs2483679	PLEKHG5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
3	chr1:10468800-10489800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:10472000-10490000	Weak transcription	Stomach Mucosa	stomach
5	chr1:10473600-10488000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:10474200-10488000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:10475600-10489600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:10475800-10490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:10477800-10490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:10477800-10490000	Weak transcription	Fetal Heart	heart
11	chr1:10478200-10488000	Weak transcription	Fetal Kidney	kidney
12	chr1:10478200-10490000	Weak transcription	Fetal Brain Male	brain
13	chr1:10478400-10488000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:10479800-10490200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:10480200-10490000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:10480200-10490000	Weak transcription	Pancreas	Pancrea
17	chr1:10480200-10490400	Weak transcription	Aorta	Aorta
18	chr1:10480400-10489600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:10480400-10489800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:10480400-10490000	Weak transcription	Colonic Mucosa	Colon
21	chr1:10480400-10490000	Weak transcription	Small Intestine	intestine
22	chr1:10480400-10490000	Weak transcription	NH-A	brain
23	chr1:10480600-10488000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:10480600-10489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:10480600-10489800	Weak transcription	Hela-S3	cervix
26	chr1:10480800-10485600	Weak transcription	HepG2	liver
27	chr1:10480800-10486400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:10480800-10487800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:10480800-10488000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:10480800-10488000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:10480800-10488000	Weak transcription	K562	blood
32	chr1:10480800-10489200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:10480800-10489600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:10480800-10489600	Weak transcription	HUVEC	blood vessel
35	chr1:10480800-10490000	Weak transcription	Placenta	Placenta
36	chr1:10480800-10490200	Weak transcription	Left Ventricle	heart
37	chr1:10481000-10488000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:10481000-10489600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:10481000-10489600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:10481000-10489800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:10481000-10490000	Weak transcription	Right Ventricle	heart
42	chr1:10481200-10489600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:10481200-10489800	Weak transcription	Osteobl	bone
44	chr1:10481200-10490000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:10481400-10488000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:10481400-10490200	Weak transcription	Ovary	ovary
47	chr1:10481600-10488000	Weak transcription	GM12878-XiMat	blood
48	chr1:10481600-10488000	Weak transcription	NHEK	skin
49	chr1:10481600-10489800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:10481600-10489800	Weak transcription	HMEC	breast

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