Variant report

Variant	rs233099
Chromosome Location	chr1:85826194-85826195
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	chr1:85823950..85826978-chr1:85828513..85831070,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1001604	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10489513	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161606	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs11161607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161610	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161611	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044537	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12047422	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12124170	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12125557	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12140103	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1498375	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1554597	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173026	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs18582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1884139	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011825	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012683	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2207368	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300637	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233050	0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233053	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233054	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233055	0.87[EUR][1000 genomes]
rs233057	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233058	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233059	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233060	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233061	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs233062	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233066	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233067	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233068	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233069	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233071	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233072	0.87[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233074	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233091	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233093	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233095	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233097	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233108	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233109	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs233112	0.87[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs233113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233114	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233115	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233118	0.87[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs233119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233120	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233121	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233124	0.87[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs233127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233130	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233131	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233132	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233133	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2474123	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs2840319	0.81[AMR][1000 genomes]
rs2892888	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3087894	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920521	0.84[AMR][1000 genomes]
rs3949301	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs423105	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949890	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs506082	0.80[EUR][1000 genomes]
rs6576761	0.84[AMR][1000 genomes]
rs6576763	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6576764	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576765	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6576766	0.81[EUR][1000 genomes]
rs6576767	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657732	0.83[GIH][hapmap]
rs6657817	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671599	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66811655	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697083	0.91[CEU][hapmap]
rs6704103	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67611930	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72724606	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729655	0.84[AMR][1000 genomes]
rs7547571	0.81[AMR][1000 genomes]
rs761601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997251	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs233099	WDR63	cis	cerebellum	SCAN
rs233099	DDAH1	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85809200-85838400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:85809400-85826800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:85809400-85826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:85809600-85828800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:85814200-85839600	Weak transcription	Left Ventricle	heart
6	chr1:85816000-85831400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:85816000-85839600	Weak transcription	Pancreas	Pancrea
8	chr1:85816400-85829000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:85816600-85826600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:85816600-85826800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:85816600-85827400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:85816600-85836800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:85816800-85826800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:85818200-85826600	Weak transcription	Fetal Intestine Large	intestine
15	chr1:85818200-85826800	Weak transcription	Fetal Stomach	stomach
16	chr1:85822800-85826600	Weak transcription	Fetal Kidney	kidney
17	chr1:85823200-85827000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:85823200-85836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:85823600-85826200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:85824000-85826200	Weak transcription	HepG2	liver
21	chr1:85824400-85826600	Enhancers	NHDF-Ad	bronchial
22	chr1:85824400-85833800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:85824600-85826400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:85824600-85827600	Enhancers	A549	lung
25	chr1:85824600-85829600	Enhancers	NHLF	lung
26	chr1:85824800-85827000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:85824800-85827600	Enhancers	HSMMtube	muscle
28	chr1:85824800-85827600	Enhancers	NH-A	brain
29	chr1:85824800-85828400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:85825000-85827200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:85825000-85827200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:85825000-85827200	Enhancers	HUVEC	blood vessel
33	chr1:85825000-85839000	Weak transcription	Aorta	Aorta
34	chr1:85825200-85828800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:85825200-85828800	Weak transcription	Psoas Muscle	Psoas
36	chr1:85825200-85830400	Enhancers	Osteobl	bone
37	chr1:85825400-85826200	Enhancers	Hela-S3	cervix
38	chr1:85825400-85827000	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:85825400-85828000	Enhancers	Colon Smooth Muscle	Colon
40	chr1:85825400-85829600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:85825600-85826200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:85825600-85826200	Enhancers	Brain Cingulate Gyrus	brain
43	chr1:85825600-85826800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:85825600-85827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:85825600-85829600	Enhancers	Fetal Lung	lung
46	chr1:85825800-85826600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:85825800-85829000	Enhancers	HSMM	muscle
48	chr1:85826000-85826200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:85826000-85826200	Enhancers	Fetal Brain Female	brain
50	chr1:85826000-85826200	Enhancers	Stomach Mucosa	stomach

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