Variant report

Variant	rs3790692
Chromosome Location	chr1:120309868-120309869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120302494..120304014-chr1:120308491..120310237,2	K562	blood:
3	chr1:120305431..120308946-chr1:120308988..120311839,5	K562	blood:

Variant related genes	Relation type
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12562383	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1441008	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1441010	0.92[CEU][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs3790693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790696	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4659233	0.89[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
3	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
4	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120307200-120312000	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:120308200-120311600	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:120308400-120310000	Enhancers	Brain Substantia Nigra	brain
8	chr1:120308400-120310000	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr1:120308400-120310400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:120308400-120310600	Enhancers	Brain Hippocampus Middle	brain
11	chr1:120308400-120311800	Active TSS	Colonic Mucosa	Colon
12	chr1:120308600-120310200	Enhancers	Small Intestine	intestine
13	chr1:120308800-120310000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:120308800-120310000	Enhancers	Colon Smooth Muscle	Colon
15	chr1:120308800-120310200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:120308800-120310200	Enhancers	Fetal Kidney	kidney
17	chr1:120308800-120310200	Flanking Active TSS	Fetal Stomach	stomach
18	chr1:120308800-120310200	Enhancers	Pancreas	Pancrea
19	chr1:120308800-120311200	Active TSS	Liver	Liver
20	chr1:120308800-120311800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:120309000-120312000	Enhancers	Fetal Lung	lung
22	chr1:120309200-120310000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:120309200-120310000	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:120309200-120310200	Enhancers	Gastric	stomach
25	chr1:120309200-120311400	Weak transcription	Fetal Heart	heart
26	chr1:120309400-120310200	Flanking Active TSS	HepG2	liver
27	chr1:120309400-120311400	Weak transcription	Right Atrium	heart
28	chr1:120309400-120311800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:120309600-120310000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:120309600-120310000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:120309600-120310000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:120309600-120310000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:120309600-120310400	Enhancers	Esophagus	oesophagus
34	chr1:120309600-120310800	Enhancers	Left Ventricle	heart
35	chr1:120309600-120311400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:120309800-120310000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:120309800-120310200	Flanking Active TSS	Stomach Mucosa	stomach
38	chr1:120309800-120310400	Enhancers	Lung	lung
39	chr1:120309800-120310800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:120309800-120311200	Weak transcription	Adipose Nuclei	Adipose
41	chr1:120309800-120311400	Weak transcription	Ovary	ovary
42	chr1:120309800-120311600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:120309800-120311600	Active TSS	Fetal Intestine Small	intestine
44	chr1:120309800-120313800	Weak transcription	Brain Anterior Caudate	brain
45	chr1:120309800-120316000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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