Variant report

Variant	rs1166704
Chromosome Location	chr1:78366894-78366895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78365940..78368034-chr1:78468691..78470675,2	K562	blood:
2	chr1:78365771..78367386-chr1:78395199..78396952,2	K562	blood:
3	chr1:78290654..78291750-chr1:78366230..78366976,4	MCF-7	breast:
4	chr1:78366287..78367159-chr1:78579821..78580485,2	K562	blood:
5	chr1:78365620..78368344-chr1:78369014..78371823,2	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10437022	0.81[CHB][hapmap];0.82[AMR][1000 genomes]
rs10873956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10873960	0.82[AMR][1000 genomes]
rs11162390	0.86[EUR][1000 genomes]
rs11162400	0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes]
rs11162403	0.86[AMR][1000 genomes]
rs11162406	0.80[AMR][1000 genomes]
rs1166697	0.89[AMR][1000 genomes]
rs1166701	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1166702	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1166705	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166707	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11805735	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11807240	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12021502	1.00[CEU][hapmap]
rs12146104	0.84[AMR][1000 genomes]
rs12405212	0.81[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12409561	0.81[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs12723748	0.84[AMR][1000 genomes]
rs1335481	0.81[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap]
rs1536160	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1539737	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1555798	0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes]
rs1616949	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1626757	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17383213	0.81[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes]
rs17387365	0.81[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes]
rs2154138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274124	1.00[CEU][hapmap]
rs2274257	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs2296453	0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes]
rs3767028	0.81[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4370803	0.82[AMR][1000 genomes]
rs4372306	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4949828	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4949829	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs57421725	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6424640	0.84[AMR][1000 genomes]
rs6424650	0.82[AMR][1000 genomes]
rs6424660	0.82[AMR][1000 genomes]
rs661038	0.95[GIH][hapmap]
rs6656888	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs6659045	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667733	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7417104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs750720	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9324166	0.89[AMR][1000 genomes]
rs9659938	0.88[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9661193	0.89[AMR][1000 genomes]

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	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
2	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
3	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
4	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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78355800-78383800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:78355800-78386200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78356200-78408600	Weak transcription	HMEC	breast
4	chr1:78356400-78396000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:78357400-78384400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:78357800-78371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:78359200-78382400	Weak transcription	Left Ventricle	heart
8	chr1:78359800-78383800	Weak transcription	Fetal Lung	lung
9	chr1:78360600-78384200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78361800-78369400	Weak transcription	Psoas Muscle	Psoas
11	chr1:78361800-78372400	Weak transcription	Pancreas	Pancrea
12	chr1:78362400-78369400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:78362400-78383200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:78362400-78383800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:78362400-78384000	Weak transcription	Fetal Stomach	stomach
16	chr1:78365400-78367000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:78365400-78367000	Enhancers	Fetal Heart	heart
18	chr1:78365400-78367000	Enhancers	HUVEC	blood vessel
19	chr1:78365600-78367000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:78365600-78367600	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:78365600-78367600	Active TSS	Right Atrium	heart
22	chr1:78365600-78367600	Active TSS	Right Ventricle	heart
23	chr1:78365800-78367600	Enhancers	Colon Smooth Muscle	Colon
24	chr1:78366000-78367000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:78366400-78367000	Enhancers	HSMMtube	muscle
26	chr1:78366600-78369000	Strong transcription	HSMM	muscle
27	chr1:78366600-78371600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:78366800-78367400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:78366800-78367600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:78366800-78368000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:78366800-78369600	Strong transcription	NH-A	brain
32	chr1:78366800-78371200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:78366800-78372400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:78366800-78375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:78366800-78381400	Weak transcription	Osteobl	bone
36	chr1:78366800-78382600	Weak transcription	NHLF	lung
37	chr1:78366800-78383600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:78366800-78383800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:78366800-78384000	Weak transcription	Aorta	Aorta

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