Variant report

Variant	rs12723684
Chromosome Location	chr1:77685042-77685043
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	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:
2	chr1:77684507..77685215-chr5:44808668..44809523,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000251141	Chromatin interaction
ENSG00000154027	Chromatin interaction
ENSG00000112996	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

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]
rs10518551	1.00[JPT][hapmap]
rs10518553	1.00[JPT][hapmap]
rs1098120	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1098121	0.87[AFR][1000 genomes]
rs1098125	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]
rs1098129	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs1098130	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1098132	0.86[AFR][1000 genomes]
rs1098133	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103683	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs1253224	0.87[AFR][1000 genomes]
rs1253226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1266316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270993	0.93[YRI][hapmap];0.89[AFR][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]
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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs1615806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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]
rs17100530	1.00[JPT][hapmap]
rs1721127	0.85[AFR][1000 genomes]
rs1721140	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1721145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1721151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371324	1.00[JPT][hapmap]
rs17379910	1.00[JPT][hapmap]
rs17380099	1.00[JPT][hapmap]
rs1779170	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1779174	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779186	0.83[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs1779189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653469	1.00[MEX][hapmap]
rs2689666	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689674	1.00[MEX][hapmap]
rs2689675	1.00[MEX][hapmap]
rs2689678	0.90[AFR][1000 genomes]
rs2689679	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs2689682	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762882	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882289	1.00[JPT][hapmap]
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]
rs4402168	1.00[JPT][hapmap]
rs58293665	0.96[AMR][1000 genomes];0.91[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]
rs6703133	1.00[JPT][hapmap]
rs67263641	0.86[AFR][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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	1.00[MEX][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839795	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]
rs839797	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839813	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]
rs839814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839823	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839824	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs839826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839827	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839830	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839831	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs858447	0.82[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][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	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
2	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
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77682800-77686400	Active TSS	GM12878-XiMat	blood
2	chr1:77683600-77686200	Active TSS	K562	blood
3	chr1:77683800-77686000	Active TSS	NHLF	lung
4	chr1:77683800-77686200	Active TSS	A549	lung
5	chr1:77684000-77685400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:77684000-77685800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:77684000-77685800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:77684000-77686000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:77684000-77686000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:77684000-77686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:77684000-77686000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:77684000-77686000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:77684000-77686000	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:77684000-77686000	Active TSS	Thymus	Thymus
15	chr1:77684000-77686200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:77684000-77686200	Active TSS	NHDF-Ad	bronchial
19	chr1:77684000-77686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:77684200-77685600	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr1:77684200-77685600	Active TSS	Brain Angular Gyrus	brain
22	chr1:77684200-77685600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:77684200-77685800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:77684200-77685800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:77684200-77685800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:77684200-77685800	Active TSS	Fetal Stomach	stomach
27	chr1:77684200-77685800	Active TSS	Left Ventricle	heart
28	chr1:77684200-77685800	Active TSS	Placenta Amnion	Placenta Amnion
29	chr1:77684200-77685800	Active TSS	Psoas Muscle	Psoas
30	chr1:77684200-77685800	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:77684200-77685800	Active TSS	Right Atrium	heart
32	chr1:77684200-77685800	Active TSS	Hela-S3	cervix
33	chr1:77684200-77685800	Active TSS	HSMMtube	muscle
34	chr1:77684200-77685800	Active TSS	NHEK	skin
35	chr1:77684200-77686000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:77684200-77686000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:77684200-77686000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:77684200-77686000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:77684200-77686000	Active TSS	Brain Germinal Matrix	brain
40	chr1:77684200-77686000	Active TSS	Fetal Intestine Large	intestine
41	chr1:77684200-77686000	Active TSS	Fetal Intestine Small	intestine
42	chr1:77684200-77686000	Active TSS	Fetal Kidney	kidney
43	chr1:77684200-77686000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:77684200-77686000	Active TSS	Fetal Muscle Leg	muscle
45	chr1:77684200-77686000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:77684200-77686000	Active TSS	Stomach Smooth Muscle	stomach
47	chr1:77684200-77686200	Active TSS	HMEC	breast
48	chr1:77684200-77686400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:77684200-77686400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:77684400-77685200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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