Variant report

Variant	rs1001604
Chromosome Location	chr1:85879524-85879525
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1006988	0.86[AFR][1000 genomes]
rs10489513	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11161606	0.81[CEU][hapmap]
rs11161607	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161610	0.83[EUR][1000 genomes]
rs11161611	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1146379	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146382	0.85[CEU][hapmap]
rs12044537	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12047422	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12124170	0.84[EUR][1000 genomes]
rs12125557	0.90[EUR][1000 genomes]
rs12140103	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1498373	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1498375	0.83[EUR][1000 genomes]
rs1554597	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs173026	0.83[EUR][1000 genomes]
rs18582	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1884139	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2011825	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2012683	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2037594	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs2177461	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2207368	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2268667	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2300634	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2300637	0.84[EUR][1000 genomes]
rs233047	0.86[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233050	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233053	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs233054	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233055	0.83[EUR][1000 genomes]
rs233057	0.83[EUR][1000 genomes]
rs233058	0.83[EUR][1000 genomes]
rs233059	0.83[EUR][1000 genomes]
rs233060	0.83[EUR][1000 genomes]
rs233061	0.87[EUR][1000 genomes]
rs233062	0.83[EUR][1000 genomes]
rs233066	0.84[EUR][1000 genomes]
rs233067	0.84[EUR][1000 genomes]
rs233068	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233069	0.85[EUR][1000 genomes]
rs233071	0.85[EUR][1000 genomes]
rs233072	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs233093	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233095	0.84[EUR][1000 genomes]
rs233097	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233099	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233108	0.83[EUR][1000 genomes]
rs233109	0.88[EUR][1000 genomes]
rs233112	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs233113	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs233114	0.83[EUR][1000 genomes]
rs233115	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs233118	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs233119	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs233120	0.82[EUR][1000 genomes]
rs233121	0.83[EUR][1000 genomes]
rs233124	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs233127	0.83[EUR][1000 genomes]
rs233130	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs233131	0.83[EUR][1000 genomes]
rs233132	0.83[EUR][1000 genomes]
rs233133	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2474123	0.89[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs2892888	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3087894	0.83[EUR][1000 genomes]
rs3768227	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs3949301	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs423105	0.83[EUR][1000 genomes]
rs4949890	0.84[EUR][1000 genomes]
rs4949900	0.89[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506082	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6576761	0.81[AFR][1000 genomes]
rs6576763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6576764	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576765	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576766	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6576767	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657817	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671599	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66811655	0.83[EUR][1000 genomes]
rs6697083	0.83[CEU][hapmap]
rs6704103	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67611930	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72724606	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs729655	0.85[AFR][1000 genomes]
rs7525786	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7539738	0.80[AFR][1000 genomes]
rs7555670	0.84[AFR][1000 genomes]
rs761601	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs997251	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][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	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
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85873200-85879600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:85873400-85882800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:85873800-85882000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
6	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:85874000-85903800	Weak transcription	NHLF	lung
8	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:85874400-85903600	Weak transcription	HepG2	liver
10	chr1:85874400-85904200	Weak transcription	NH-A	brain
11	chr1:85875000-85882800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:85875400-85880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:85875400-85885600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:85876800-85880000	Strong transcription	HSMM	muscle
15	chr1:85877000-85880400	Enhancers	NHDF-Ad	bronchial
16	chr1:85877200-85885600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:85877400-85882400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:85877600-85882400	Weak transcription	Psoas Muscle	Psoas
19	chr1:85877600-85882800	Weak transcription	Aorta	Aorta
20	chr1:85877600-85882800	Weak transcription	Pancreas	Pancrea
21	chr1:85877600-85882800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:85877600-85885800	Weak transcription	HSMMtube	muscle
23	chr1:85877800-85882600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:85878000-85883800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:85878200-85880600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:85878200-85882600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:85878400-85879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:85878400-85879800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:85878400-85880200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:85878400-85880400	Enhancers	Osteobl	bone
31	chr1:85878400-85883000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:85878800-85879800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:85878800-85880600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:85879000-85882800	Weak transcription	Ovary	ovary
35	chr1:85879200-85879600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85879200-85880000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:85879200-85880400	Enhancers	HUVEC	blood vessel
38	chr1:85879200-85885600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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