Variant report

Variant	rs1539739
Chromosome Location	chr1:78266417-78266418
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	chr1:78220754..78222888-chr1:78264433..78266757,2	K562	blood:
2	chr1:78220754..78225249-chr1:78263439..78267334,4	K562	blood:

Variant related genes	Relation type
ENSG00000077254	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1038983	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs10873951	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs10873953	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873954	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873955	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11162368	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162370	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162374	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11162378	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11162380	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11162383	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162384	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162386	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162387	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578805	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1166586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1166589	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12090729	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132838	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12135104	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12142441	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12717768	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389789	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389790	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs166770	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2031342	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203229	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2088058	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2296227	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278832	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278834	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs278837	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278840	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278841	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278842	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278844	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278848	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278850	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs278851	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278855	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278856	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278858	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs278859	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs278860	0.87[CHD][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278863	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278864	0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs370335	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3767037	0.95[CEU][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767038	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4488068	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949817	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4949818	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4949822	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56688304	0.85[ASN][1000 genomes]
rs574973	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6603956	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs6603958	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6603960	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6657290	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs6661656	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6672200	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6687501	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6687596	0.85[ASN][1000 genomes]
rs6699205	0.95[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6699311	0.90[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs717333	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519946	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7535781	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7536206	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543037	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543125	1.00[ASN][1000 genomes]
rs7546365	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7556227	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556523	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8179272	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872342	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9662527	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs9988619	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
3	chr1:78246200-78272000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78246200-78272800	Weak transcription	Psoas Muscle	Psoas
5	chr1:78246200-78279400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:78246200-78279600	Weak transcription	Aorta	Aorta
7	chr1:78246400-78272400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:78246400-78273200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:78246400-78274000	Weak transcription	Fetal Kidney	kidney
10	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
11	chr1:78246600-78274200	Weak transcription	HMEC	breast
12	chr1:78247400-78278400	Weak transcription	Hela-S3	cervix
13	chr1:78247600-78272400	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
15	chr1:78249200-78271400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:78250400-78282400	Weak transcription	NHEK	skin
17	chr1:78250600-78279000	Weak transcription	NHLF	lung
18	chr1:78250800-78268000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:78252000-78272600	Weak transcription	Spleen	Spleen
20	chr1:78252000-78272800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:78252200-78282600	Weak transcription	Right Ventricle	heart
22	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
23	chr1:78252800-78272800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:78253000-78266800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:78253000-78267200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:78253000-78267800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:78253000-78272800	Weak transcription	Thymus	Thymus
28	chr1:78253000-78273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:78253000-78279400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:78253000-78283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:78253600-78269800	Weak transcription	Brain Germinal Matrix	brain
32	chr1:78254400-78267800	Weak transcription	Fetal Lung	lung
33	chr1:78254400-78272800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:78254400-78274000	Weak transcription	HSMMtube	muscle
35	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:78254600-78267200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:78254600-78268400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:78254600-78269000	Weak transcription	Fetal Brain Male	brain
39	chr1:78254600-78271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:78254600-78272000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:78254600-78272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:78255000-78272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:78255200-78267600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:78255400-78269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:78255600-78267600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:78255600-78267800	Weak transcription	Placenta	Placenta
47	chr1:78255600-78271400	Weak transcription	Fetal Brain Female	brain
48	chr1:78255800-78267200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:78256600-78267600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:78256600-78271400	Weak transcription	Lung	lung

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