Variant report

Variant	rs11809524
Chromosome Location	chr1:103459537-103459538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 177 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1012282	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10458505	0.96[ASN][1000 genomes]
rs10493988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10493991	1.00[JPT][hapmap]
rs10782921	1.00[JPT][hapmap]
rs10874665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10874668	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10874679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11164649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11164650	0.96[ASN][1000 genomes]
rs11164653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11164657	0.88[ASN][1000 genomes]
rs11164658	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11164662	0.88[CHB][hapmap]
rs11164665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164669	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11164672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11811018	1.00[JPT][hapmap]
rs12025848	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12036215	0.88[ASN][1000 genomes]
rs12042830	0.92[ASN][1000 genomes]
rs12043105	0.96[ASN][1000 genomes]
rs12047268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12092111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12118365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	1.00[JPT][hapmap]
rs12136338	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1241162	1.00[JPT][hapmap]
rs1241166	1.00[JPT][hapmap]
rs1241181	1.00[JPT][hapmap]
rs1241182	1.00[JPT][hapmap]
rs1241183	1.00[JPT][hapmap]
rs12723167	1.00[JPT][hapmap]
rs12723922	1.00[JPT][hapmap]
rs12724152	1.00[JPT][hapmap]
rs12726958	1.00[JPT][hapmap]
rs12727959	1.00[JPT][hapmap]
rs12728397	1.00[JPT][hapmap]
rs12729449	1.00[JPT][hapmap]
rs12729602	0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12731843	1.00[JPT][hapmap]
rs12733933	1.00[JPT][hapmap]
rs12738133	1.00[JPT][hapmap]
rs12743365	1.00[JPT][hapmap]
rs12744290	1.00[JPT][hapmap]
rs12744488	1.00[JPT][hapmap]
rs12750377	1.00[JPT][hapmap]
rs12755987	0.96[ASN][1000 genomes]
rs12756627	1.00[JPT][hapmap]
rs1337174	1.00[JPT][hapmap]
rs1337175	1.00[JPT][hapmap]
rs1337186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415359	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463034	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1463035	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1463037	1.00[JPT][hapmap]
rs1463038	1.00[JPT][hapmap]
rs1463039	1.00[JPT][hapmap]
rs1538041	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1564143	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1564144	1.00[ASN][1000 genomes]
rs1572515	0.88[ASN][1000 genomes]
rs1591636	1.00[JPT][hapmap]
rs1591637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1621055	1.00[JPT][hapmap]
rs1622838	1.00[JPT][hapmap]
rs1676493	1.00[JPT][hapmap]
rs1676494	0.82[JPT][hapmap]
rs1676497	1.00[JPT][hapmap]
rs1676498	1.00[JPT][hapmap]
rs1676499	1.00[JPT][hapmap]
rs1676500	1.00[JPT][hapmap]
rs1676501	1.00[JPT][hapmap]
rs1676502	1.00[JPT][hapmap]
rs17506286	1.00[JPT][hapmap]
rs17507967	1.00[JPT][hapmap]
rs1763344	1.00[JPT][hapmap]
rs1763345	1.00[JPT][hapmap]
rs1763346	1.00[JPT][hapmap]
rs1824691	1.00[ASN][1000 genomes]
rs1870958	1.00[JPT][hapmap]
rs1903787	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1966959	1.00[ASN][1000 genomes]
rs2050601	1.00[JPT][hapmap]
rs2061704	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2065922	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2252146	1.00[JPT][hapmap]
rs2254082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2376280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2376281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2615977	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2615987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2615999	1.00[JPT][hapmap]
rs2622844	0.96[ASN][1000 genomes]
rs2622846	1.00[ASN][1000 genomes]
rs2622848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2622854	1.00[ASN][1000 genomes]
rs2622870	1.00[JPT][hapmap]
rs2622873	0.96[ASN][1000 genomes]
rs2622874	1.00[JPT][hapmap]
rs2622876	1.00[JPT][hapmap]
rs2622877	1.00[JPT][hapmap]
rs2622880	1.00[JPT][hapmap]
rs2783570	1.00[JPT][hapmap]
rs2786120	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2786121	1.00[JPT][hapmap]
rs2786122	1.00[JPT][hapmap]
rs2786125	1.00[JPT][hapmap]
rs2929163	1.00[JPT][hapmap]
rs3102053	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34765476	0.81[CHD][hapmap]
rs3767272	0.82[JPT][hapmap]
rs3850459	1.00[JPT][hapmap]
rs3908854	0.88[ASN][1000 genomes]
rs4098282	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4338381	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4478834	1.00[JPT][hapmap]
rs4907986	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908280	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4908281	1.00[ASN][1000 genomes]
rs4908286	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6663034	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6670486	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6672647	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6695665	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6699118	1.00[ASN][1000 genomes]
rs7517682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7532572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7544130	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7550118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7552614	1.00[ASN][1000 genomes]
rs945748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs986944	1.00[ASN][1000 genomes]
rs9970114	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv871929	chr1:103393457-103466917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv871067	chr1:103407999-103509323	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv871736	chr1:103409100-103548497	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv870521	chr1:103409558-103466917	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv871567	chr1:103416690-103499049	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	esv2755977	chr1:103427381-103459537	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv871657	chr1:103427381-103528128	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv871198	chr1:103432687-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv546935	chr1:103438795-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv462772	chr1:103438795-103499896	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv546936	chr1:103438795-103499896	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv462783	chr1:103438795-103548497	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv546937	chr1:103438795-103548497	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv462794	chr1:103450196-103539007	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv546938	chr1:103450196-103539007	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv871286	chr1:103455217-103528128	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
33	nsv871733	chr1:103459537-103509323	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103369600-103498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103386200-103482000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:103400200-103462000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:103415800-103485200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:103423000-103468200	Weak transcription	HSMMtube	muscle
6	chr1:103423800-103476000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:103425000-103478000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:103446800-103497800	Weak transcription	HSMM	muscle
9	chr1:103449200-103545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:103450800-103470200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:103453200-103467400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:103453400-103490000	Weak transcription	NH-A	brain
13	chr1:103454000-103468400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:103457200-103459800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:103457200-103462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:103458600-103460800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:103459000-103460200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:103459200-103461800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:103459400-103460600	Weak transcription	Brain Inferior Temporal Lobe	brain

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