Variant report

Variant	rs1098125
Chromosome Location	chr1:77640166-77640167
allele	A/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:92)

rs_ID	r²[population]
rs10493598	1.00[ASN][1000 genomes]
rs10493600	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1098120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1098130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1098133	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1266316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722930	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723684	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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724800	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733382	1.00[ASN][1000 genomes]
rs12733865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735141	1.00[ASN][1000 genomes]
rs12736701	1.00[JPT][hapmap]
rs12736719	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12737795	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12743614	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12751439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12755514	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760157	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419249	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502529	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs1502533	0.93[YRI][hapmap]
rs1615806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099870	1.00[ASN][1000 genomes]
rs17100022	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1721140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1721145	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]
rs1721151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779170	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1779174	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779186	1.00[MEX][hapmap]
rs1779189	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779198	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833041	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069225	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2653465	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653469	0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2689666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689674	0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs2689675	0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs2689682	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762882	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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882290	1.00[ASN][1000 genomes]
rs34377928	1.00[ASN][1000 genomes]
rs34615286	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667818	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34797011	1.00[ASN][1000 genomes]
rs35221798	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35480396	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35742892	0.86[ASN][1000 genomes]
rs35799710	1.00[ASN][1000 genomes]
rs36039369	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36132025	1.00[ASN][1000 genomes]
rs58293665	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60388613	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60836923	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700145	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71588888	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71658782	0.80[EUR][1000 genomes]
rs71658783	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71658784	1.00[ASN][1000 genomes]
rs71658785	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71658787	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71658788	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092422	1.00[ASN][1000 genomes]
rs74092428	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092429	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092432	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092466	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522727	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7524360	0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs7531788	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541431	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839797	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839799	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs839800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839814	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839823	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];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839827	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839830	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858447	1.00[MEX][hapmap]

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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77595400-77640400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:77606200-77651600	Weak transcription	Aorta	Aorta
3	chr1:77616200-77663200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:77619000-77640200	Weak transcription	A549	lung
5	chr1:77621000-77641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:77623400-77641000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:77626000-77640600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:77626000-77662600	Weak transcription	Thymus	Thymus
9	chr1:77626000-77684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:77626800-77668000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:77626800-77674800	Weak transcription	Ovary	ovary
12	chr1:77626800-77676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:77627200-77641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:77629000-77642000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:77630400-77641200	Weak transcription	NH-A	brain
16	chr1:77630800-77640200	Weak transcription	Primary B cells from cord blood	blood
17	chr1:77630800-77641200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:77630800-77652000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:77630800-77660600	Weak transcription	Left Ventricle	heart
20	chr1:77631800-77660600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:77632800-77640800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:77634400-77656600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:77636600-77640200	Weak transcription	Osteobl	bone
24	chr1:77636800-77640200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:77637800-77640400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:77637800-77647800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:77638200-77662200	Weak transcription	Small Intestine	intestine
28	chr1:77639200-77640600	ZNF genes & repeats	Dnd41	blood
29	chr1:77639400-77640200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:77639400-77640400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr1:77639400-77640600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr1:77639400-77645800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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