Variant report

Variant	rs1676488
Chromosome Location	chr1:103390327-103390328
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1026660	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10493985	1.00[MEX][hapmap]
rs10493987	1.00[CEU][hapmap]
rs10747435	1.00[CEU][hapmap]
rs10782915	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10782916	1.00[CEU][hapmap]
rs10782920	1.00[CEU][hapmap]
rs11164647	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1241167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1271797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1337192	1.00[CEU][hapmap]
rs1415350	1.00[CEU][hapmap]
rs1463040	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463044	0.87[EUR][1000 genomes]
rs1463047	1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1564141	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1564142	0.87[EUR][1000 genomes]
rs1676490	0.94[EUR][1000 genomes]
rs1676492	0.87[EUR][1000 genomes]
rs1676503	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1676504	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17101127	1.00[CEU][hapmap]
rs17127490	1.00[CEU][hapmap]
rs1763351	1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1763360	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061709	0.87[EUR][1000 genomes]
rs2199553	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2615976	1.00[CEU][hapmap]
rs2615991	1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2615994	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2616000	0.87[EUR][1000 genomes]
rs2616008	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2616009	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2616012	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2616013	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2622836	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2622837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2622841	1.00[CEU][hapmap]
rs2622849	1.00[CEU][hapmap]
rs2622861	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2622862	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2622863	1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2622864	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2622867	1.00[CEU][hapmap]
rs2622868	1.00[CEU][hapmap]
rs2622883	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2786124	1.00[CEU][hapmap]
rs2929161	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs2929162	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs3102057	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3126210	0.87[EUR][1000 genomes]
rs3126211	0.87[EUR][1000 genomes]
rs3126212	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3126213	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3126215	1.00[CEU][hapmap]
rs3908855	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs4908279	0.87[EUR][1000 genomes]
rs6577342	1.00[CEU][hapmap]
rs6577353	1.00[CEU][hapmap]
rs6667609	1.00[CEU][hapmap]
rs6674148	1.00[CEU][hapmap]
rs7523441	1.00[CEU][hapmap]
rs7531081	1.00[CEU][hapmap]
rs7544444	1.00[CEU][hapmap]
rs7544816	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs9434362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs981961	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs984023	0.87[EUR][1000 genomes]
rs992098	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs992099	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871809	chr1:103339272-103459537	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv871732	chr1:103339272-103466917	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv462728	chr1:103342392-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546930	chr1:103342392-103455217	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv870835	chr1:103349419-103409100	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv871533	chr1:103349419-103412000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv870487	chr1:103349419-103466917	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv871019	chr1:103350903-103466917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv870601	chr1:103352451-103409100	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv870881	chr1:103352451-103416690	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv870952	chr1:103352451-103432687	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv871807	chr1:103352451-103450196	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv871335	chr1:103352451-103459537	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv870644	chr1:103352451-103466917	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv871741	chr1:103352451-103517428	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv462739	chr1:103354138-103402184	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv546931	chr1:103354138-103402184	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv871194	chr1:103354138-103416690	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv871970	chr1:103354138-103450196	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv871494	chr1:103354138-103466917	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv462761	chr1:103356168-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv546933	chr1:103356168-103455217	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv870607	chr1:103362909-103528128	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv532548	chr1:103381480-103431911	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv871840	chr1:103384610-103455217	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv870995	chr1:103384610-103548497	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103352600-103403200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:103369600-103498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:103378800-103400000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:103380000-103399000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:103380800-103393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:103381200-103399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:103382200-103393000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:103385800-103401000	Weak transcription	HSMM	muscle
9	chr1:103386000-103407000	Weak transcription	NH-A	brain
10	chr1:103386200-103393000	Weak transcription	Osteobl	bone
11	chr1:103386200-103399600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:103386200-103482000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:103387000-103394400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:103387400-103392800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:103388800-103392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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