Variant report

Variant	rs6604088
Chromosome Location	chr1:92766848-92766849
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	chr1:92763308..92766374-chr1:92766490..92770872,7	K562	blood:

Variant related genes	Relation type
ENSG00000122484	Chromatin interaction
ENSG00000174842	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10747503	0.80[ASN][1000 genomes]
rs10875319	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875349	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164226	0.90[ASN][1000 genomes]
rs11164288	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164312	0.90[ASN][1000 genomes]
rs11164349	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164546	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]
rs11803457	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024731	0.90[ASN][1000 genomes]
rs12086394	0.86[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]
rs1325435	0.84[EUR][1000 genomes]
rs1483022	0.80[ASN][1000 genomes]
rs1487536	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487540	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542685	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809606	0.90[ASN][1000 genomes]
rs1872007	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004814	0.90[ASN][1000 genomes]
rs2046620	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087194	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391158	0.90[ASN][1000 genomes]
rs2391161	0.92[EUR][1000 genomes]
rs2391162	0.90[ASN][1000 genomes]
rs3103170	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3103176	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103181	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118137	0.80[ASN][1000 genomes]
rs3122321	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122323	0.81[EUR][1000 genomes]
rs3122325	0.80[EUR][1000 genomes]
rs3122327	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131813	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131814	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131827	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131828	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34090353	0.90[ASN][1000 genomes]
rs35580949	0.90[ASN][1000 genomes]
rs3929737	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393167	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658300	0.91[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	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603971	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604082	0.80[ASN][1000 genomes]
rs6604090	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661384	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662379	0.90[ASN][1000 genomes]
rs6663114	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6663118	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663278	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663905	0.90[ASN][1000 genomes]
rs6668803	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689366	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692287	0.90[EUR][1000 genomes]
rs6702267	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720457	0.90[ASN][1000 genomes]
rs733012	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745793	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517541	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518974	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520275	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524120	0.90[ASN][1000 genomes]
rs7539757	0.90[ASN][1000 genomes]
rs7543947	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550680	0.90[ASN][1000 genomes]
rs912794	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439911	0.90[ASN][1000 genomes]
rs9440085	0.92[EUR][1000 genomes]
rs9943178	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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	chr1:92762800-92767200	Active TSS	GM12878-XiMat	blood
2	chr1:92765200-92791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:92765200-92792000	Weak transcription	Aorta	Aorta
4	chr1:92765200-92792000	Weak transcription	Esophagus	oesophagus
5	chr1:92765400-92767800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:92765400-92769400	Weak transcription	Placenta	Placenta
7	chr1:92765400-92772200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:92765600-92767200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:92765600-92767200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:92765600-92767800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:92765600-92768400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:92765600-92768800	Weak transcription	HSMM	muscle
13	chr1:92765600-92769400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:92765600-92769600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:92765600-92770000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:92765600-92770000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:92765600-92770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:92765600-92770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:92765600-92770200	Weak transcription	Colonic Mucosa	Colon
20	chr1:92765600-92770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:92765600-92770200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:92765600-92772200	Weak transcription	Left Ventricle	heart
23	chr1:92765600-92775600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:92765600-92777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:92765600-92778400	Weak transcription	Fetal Stomach	stomach
26	chr1:92765600-92789600	Weak transcription	Psoas Muscle	Psoas
27	chr1:92765600-92791000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:92765600-92791600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:92765600-92791800	Weak transcription	Lung	lung
30	chr1:92765600-92791800	Weak transcription	Pancreas	Pancrea
31	chr1:92765600-92791800	Weak transcription	Right Ventricle	heart
32	chr1:92765600-92792000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:92765600-92792000	Weak transcription	Spleen	Spleen
34	chr1:92765800-92767200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:92765800-92767200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:92765800-92767400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:92765800-92767400	Enhancers	Fetal Heart	heart
38	chr1:92765800-92768800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:92765800-92768800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:92765800-92769000	Weak transcription	NHDF-Ad	bronchial
41	chr1:92765800-92769200	Weak transcription	Fetal Thymus	thymus
42	chr1:92765800-92769400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:92765800-92769400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:92765800-92769400	Weak transcription	A549	lung
45	chr1:92765800-92769400	Weak transcription	HUVEC	blood vessel
46	chr1:92765800-92770000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:92765800-92770200	Weak transcription	Primary B cells from cord blood	blood
48	chr1:92765800-92770400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:92765800-92773400	Weak transcription	NHLF	lung
50	chr1:92765800-92773600	Weak transcription	Thymus	Thymus

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