Variant report

Variant	rs6685892
Chromosome Location	chr1:120458004-120458005
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:120457910-120458681	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120455729..120458677-chr1:120465147..120468544,4	MCF-7	breast:
2	chr1:120456262..120460550-chr1:120460767..120463877,3	K562	blood:

Variant related genes	Relation type
ENSG00000261662	TF binding region
ENSG00000134250	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10127888	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923931	0.80[CEU][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493691	0.85[AFR][1000 genomes]
rs1493694	0.80[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738647	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027447	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453040	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	0.80[EUR][1000 genomes]
rs2453058	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493389	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493390	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493391	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493392	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493394	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493413	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493415	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641317	0.80[CEU][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641348	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641352	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793829	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793831	0.80[CEU][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934381	0.80[CEU][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934387	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897478	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406767	0.82[ASN][1000 genomes]
rs56302051	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668119	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs699779	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72697237	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515431	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534585	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534586	0.80[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835576	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv547625	chr1:120422705-120466108	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv2610	chr1:120451060-120471049	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120448200-120471000	Weak transcription	Right Atrium	heart
2	chr1:120450000-120473000	Strong transcription	HSMM	muscle
3	chr1:120450200-120458600	Weak transcription	HepG2	liver
4	chr1:120451000-120458400	Weak transcription	Small Intestine	intestine
5	chr1:120451000-120466800	Weak transcription	Fetal Brain Male	brain
6	chr1:120451600-120480000	Weak transcription	Psoas Muscle	Psoas
7	chr1:120452000-120485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:120452600-120472800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:120452800-120460000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:120453000-120473200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:120453000-120476400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:120453000-120483600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:120453200-120475600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:120453400-120472600	Strong transcription	Osteobl	bone
15	chr1:120453400-120476400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:120453600-120458400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:120454200-120469200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:120454400-120471600	Strong transcription	NH-A	brain
19	chr1:120454400-120472400	Strong transcription	NHDF-Ad	bronchial
20	chr1:120454400-120472600	Strong transcription	Primary B cells from cord blood	blood
21	chr1:120454800-120472800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:120454800-120473200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:120455200-120460000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:120455200-120460000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:120455200-120472000	Strong transcription	Placenta	Placenta
26	chr1:120455400-120460600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:120455400-120467600	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:120455400-120472200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:120455400-120472800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr1:120455400-120472800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:120455400-120472800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:120455400-120472800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:120455400-120475800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:120455600-120458600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:120455600-120460000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:120455600-120466800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:120455600-120467600	Strong transcription	Adipose Nuclei	Adipose
38	chr1:120455600-120470000	Strong transcription	Esophagus	oesophagus
39	chr1:120455600-120472000	Strong transcription	Fetal Lung	lung
40	chr1:120455600-120472200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:120455600-120472600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:120455600-120472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:120455600-120472800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:120455600-120473400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:120455600-120474000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:120455800-120467800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:120455800-120472800	Strong transcription	NHLF	lung
48	chr1:120455800-120474200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:120455800-120486800	Strong transcription	Liver	Liver
50	chr1:120456000-120469400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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