Variant report

Variant	rs2889537
Chromosome Location	chr1:226432521-226432522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10127753	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10127776	0.95[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10127970	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753416	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799341	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10799343	0.89[EUR][1000 genomes]
rs10799344	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799345	0.81[JPT][hapmap]
rs10799346	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799347	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915962	0.85[EUR][1000 genomes]
rs10915964	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915970	0.90[EUR][1000 genomes]
rs12022311	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1219658	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1417766	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17263666	0.81[AMR][1000 genomes]
rs1813323	0.95[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2126573	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2126577	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126578	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169567	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254723	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2377026	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2377028	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2377029	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2615799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2615803	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2666429	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2927338	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4418563	0.83[EUR][1000 genomes]
rs4612598	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6605032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552015	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9725097	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9729447	0.84[AMR][1000 genomes];0.82[ASN][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	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2889537	LIN9	cis	cerebellum	SCAN
rs2889537	GJC2	cis	cerebellum	SCAN
rs2889537	ITPKB	cis	cerebellum	SCAN
rs2889537	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226412000-226449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226412000-226455400	Weak transcription	Ovary	ovary
3	chr1:226412000-226456200	Weak transcription	NH-A	brain
4	chr1:226412000-226460600	Weak transcription	Aorta	Aorta
5	chr1:226412200-226437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:226412200-226448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:226412200-226456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:226412200-226485400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:226412400-226435600	Weak transcription	Hela-S3	cervix
10	chr1:226412400-226442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:226412400-226443000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:226412400-226443000	Weak transcription	Osteobl	bone
13	chr1:226412400-226446800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:226413000-226445000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:226413000-226448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:226413200-226456200	Weak transcription	NHDF-Ad	bronchial
17	chr1:226413600-226440600	Weak transcription	Thymus	Thymus
18	chr1:226413600-226447000	Weak transcription	Brain Germinal Matrix	brain
19	chr1:226413600-226447800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:226414000-226436600	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:226414000-226456800	Weak transcription	Fetal Kidney	kidney
22	chr1:226414200-226447200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:226414200-226454400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:226414600-226457000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:226414800-226443000	Weak transcription	Placenta	Placenta
26	chr1:226414800-226484600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:226415400-226473800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:226415600-226450000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:226415800-226495400	Weak transcription	Liver	Liver
30	chr1:226416200-226495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:226416400-226457400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:226416800-226443400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:226417000-226438000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:226417400-226440400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:226418200-226437200	Weak transcription	Left Ventricle	heart
36	chr1:226418400-226455400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:226418400-226484600	Weak transcription	Right Ventricle	heart
38	chr1:226418800-226435400	Weak transcription	HUVEC	blood vessel
39	chr1:226418800-226437000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:226420800-226433800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:226421800-226438000	Weak transcription	Primary T cells from cord blood	blood
42	chr1:226421800-226457400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:226422000-226435800	Weak transcription	GM12878-XiMat	blood
44	chr1:226422000-226440200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:226422800-226445000	Weak transcription	NHLF	lung
46	chr1:226423400-226436200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:226424400-226435800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:226424400-226449800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:226425000-226433800	Weak transcription	Fetal Brain Male	brain
50	chr1:226425000-226435600	Weak transcription	Fetal Lung	lung

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