Variant report

Variant	rs6661384
Chromosome Location	chr1:92768664-92768665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92768070..92770349-chr1:92773069..92775193,2	K562	blood:
2	chr1:92764662..92766279-chr1:92768201..92769903,2	MCF-7	breast:
3	chr1:92763308..92766374-chr1:92766490..92770872,7	K562	blood:

Variant related genes	Relation type
ENSG00000174842	Chromatin interaction
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10159094	1.00[CHB][hapmap]
rs10747503	0.80[ASN][1000 genomes]
rs10875204	0.85[CHD][hapmap]
rs10875319	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875349	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164226	0.90[ASN][1000 genomes]
rs11164288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164312	0.90[ASN][1000 genomes]
rs11164349	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164546	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11577839	0.90[ASN][1000 genomes]
rs11578012	0.90[ASN][1000 genomes]
rs11578400	0.90[ASN][1000 genomes]
rs11585255	0.90[ASN][1000 genomes]
rs11586989	0.80[ASN][1000 genomes]
rs11588044	0.90[ASN][1000 genomes]
rs11589858	0.90[ASN][1000 genomes]
rs11803383	0.83[EUR][1000 genomes]
rs11803457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024731	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12086394	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094293	0.90[ASN][1000 genomes]
rs12401372	0.90[ASN][1000 genomes]
rs12407622	0.90[ASN][1000 genomes]
rs12727665	0.90[ASN][1000 genomes]
rs12731923	0.90[ASN][1000 genomes]
rs12735898	0.90[ASN][1000 genomes]
rs12740246	0.80[ASN][1000 genomes]
rs12755781	0.90[ASN][1000 genomes]
rs12757533	0.90[ASN][1000 genomes]
rs1483022	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs1487536	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487540	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809606	0.90[ASN][1000 genomes]
rs1872007	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004814	0.90[ASN][1000 genomes]
rs2046620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087194	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093879	0.85[CHD][hapmap]
rs2391158	0.90[ASN][1000 genomes]
rs2391161	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2391162	0.90[ASN][1000 genomes]
rs2893200	0.85[CHD][hapmap]
rs3103176	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118137	0.80[ASN][1000 genomes]
rs3122321	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122323	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3122325	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3122327	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131813	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131820	0.96[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs3131827	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34090353	0.90[ASN][1000 genomes]
rs35580949	0.90[ASN][1000 genomes]
rs3851271	0.85[CHD][hapmap]
rs3851272	0.85[CHD][hapmap]
rs3929737	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393167	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414050	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437922	0.85[CHD][hapmap]
rs4658128	0.85[CHD][hapmap]
rs4658300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949888	0.90[ASN][1000 genomes]
rs4970699	0.90[ASN][1000 genomes]
rs4970713	0.90[ASN][1000 genomes]
rs6603962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603971	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604082	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs6604088	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604090	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662379	0.90[ASN][1000 genomes]
rs6663114	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6663118	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663905	0.90[ASN][1000 genomes]
rs6668803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689366	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692287	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6702267	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720457	0.90[ASN][1000 genomes]
rs733012	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745793	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517541	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518974	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520275	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524120	0.90[ASN][1000 genomes]
rs7533077	0.85[CHD][hapmap]
rs7539757	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7542358	0.85[CHD][hapmap]
rs7543947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550680	0.90[ASN][1000 genomes]
rs7554154	0.82[EUR][1000 genomes]
rs912794	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439911	0.90[ASN][1000 genomes]
rs9440085	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9943178	0.93[EUR][1000 genomes];1.00[ASN][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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765200-92791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:92765200-92792000	Weak transcription	Aorta	Aorta
3	chr1:92765200-92792000	Weak transcription	Esophagus	oesophagus
4	chr1:92765400-92769400	Weak transcription	Placenta	Placenta
5	chr1:92765400-92772200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:92765600-92768800	Weak transcription	HSMM	muscle
7	chr1:92765600-92769400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:92765600-92769600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:92765600-92770000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:92765600-92770000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:92765600-92770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:92765600-92770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:92765600-92770200	Weak transcription	Colonic Mucosa	Colon
14	chr1:92765600-92770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:92765600-92770200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:92765600-92772200	Weak transcription	Left Ventricle	heart
17	chr1:92765600-92775600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:92765600-92777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:92765600-92778400	Weak transcription	Fetal Stomach	stomach
20	chr1:92765600-92789600	Weak transcription	Psoas Muscle	Psoas
21	chr1:92765600-92791000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:92765600-92791600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:92765600-92791800	Weak transcription	Lung	lung
24	chr1:92765600-92791800	Weak transcription	Pancreas	Pancrea
25	chr1:92765600-92791800	Weak transcription	Right Ventricle	heart
26	chr1:92765600-92792000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:92765600-92792000	Weak transcription	Spleen	Spleen
28	chr1:92765800-92768800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr1:92765800-92768800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:92765800-92769000	Weak transcription	NHDF-Ad	bronchial
31	chr1:92765800-92769200	Weak transcription	Fetal Thymus	thymus
32	chr1:92765800-92769400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:92765800-92769400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:92765800-92769400	Weak transcription	A549	lung
35	chr1:92765800-92769400	Weak transcription	HUVEC	blood vessel
36	chr1:92765800-92770000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:92765800-92770200	Weak transcription	Primary B cells from cord blood	blood
38	chr1:92765800-92770400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:92765800-92773400	Weak transcription	NHLF	lung
40	chr1:92765800-92773600	Weak transcription	Thymus	Thymus
41	chr1:92765800-92773600	Weak transcription	HSMMtube	muscle
42	chr1:92765800-92786200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:92765800-92789000	Weak transcription	Ovary	ovary
44	chr1:92765800-92789200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:92765800-92791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:92765800-92791800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:92765800-92791800	Weak transcription	Gastric	stomach
48	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
49	chr1:92766000-92770200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:92766000-92770200	Weak transcription	Rectal Smooth Muscle	rectum

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