Variant report

Variant	rs16987878
Chromosome Location	chr2:20797740-20797741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
2	chr2:20674239..20675822-chr2:20797261..20800126,2	MCF-7	breast:
3	chr2:20790810..20793188-chr2:20795452..20798408,2	MCF-7	breast:
4	chr2:20785117..20787518-chr2:20797517..20799254,2	MCF-7	breast:
5	chr2:20793781..20795387-chr2:20795652..20798532,2	K562	blood:
6	chr2:20794523..20801165-chr2:20801395..20807064,11	K562	blood:
7	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
8	chr2:20790477..20793225-chr2:20796841..20798820,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000233416	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10166792	0.89[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10177787	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10190705	0.84[ASN][1000 genomes]
rs10195324	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10195722	0.92[JPT][hapmap]
rs10200207	0.83[ASN][1000 genomes]
rs11096677	0.88[ASN][1000 genomes]
rs1123781	0.89[ASN][1000 genomes]
rs11691255	0.84[ASN][1000 genomes]
rs12472478	0.92[JPT][hapmap]
rs12621527	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs13422371	0.84[ASN][1000 genomes]
rs16987857	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs16987880	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16987884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2882035	0.90[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2882036	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs4666315	0.89[CEU][hapmap];0.88[ASN][1000 genomes]
rs4666429	0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4666430	0.92[JPT][hapmap]
rs4666431	0.92[JPT][hapmap]
rs55835545	1.00[ASN][1000 genomes]
rs56129345	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59169527	0.95[ASN][1000 genomes]
rs72782365	0.95[ASN][1000 genomes]
rs72782367	0.99[ASN][1000 genomes]
rs72782368	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs766474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs921601	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921602	1.00[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active 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	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
2	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20789200-20800400	Enhancers	Placenta	Placenta
4	chr2:20790200-20797800	Enhancers	Fetal Intestine Large	intestine
5	chr2:20790800-20801200	Enhancers	Adipose Nuclei	Adipose
6	chr2:20791800-20800400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:20792000-20797800	Enhancers	HSMM	muscle
8	chr2:20792000-20798200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:20792200-20797800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:20792200-20797800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:20792200-20797800	Enhancers	NH-A	brain
12	chr2:20792200-20798200	Enhancers	Ovary	ovary
13	chr2:20792400-20797800	Enhancers	Lung	lung
14	chr2:20792400-20797800	Enhancers	NHLF	lung
15	chr2:20792400-20798400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:20792400-20800200	Enhancers	Right Atrium	heart
17	chr2:20792600-20797800	Enhancers	NHDF-Ad	bronchial
18	chr2:20792800-20798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:20792800-20801800	Enhancers	HUVEC	blood vessel
20	chr2:20793000-20797800	Enhancers	Brain Hippocampus Middle	brain
21	chr2:20793000-20799000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:20793000-20800400	Enhancers	Left Ventricle	heart
23	chr2:20793000-20801200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:20793800-20801400	Enhancers	Brain Angular Gyrus	brain
25	chr2:20794200-20798000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:20794200-20800000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:20794600-20798200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:20794600-20800200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:20794800-20797800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:20794800-20798200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:20794800-20801200	Enhancers	Brain Anterior Caudate	brain
32	chr2:20794800-20801200	Enhancers	Brain Substantia Nigra	brain
33	chr2:20795000-20797800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:20795000-20801200	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:20795000-20801600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:20795000-20802000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:20795200-20798000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:20795200-20798000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr2:20795200-20799800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:20795400-20797800	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:20795400-20799800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:20795600-20797800	Enhancers	Colon Smooth Muscle	Colon
43	chr2:20795600-20798000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:20795600-20798000	Enhancers	Fetal Muscle Leg	muscle
45	chr2:20795600-20798200	Enhancers	Small Intestine	intestine
46	chr2:20795600-20799000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:20795600-20800000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:20795600-20800200	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:20795600-20800200	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:20795800-20799000	Weak transcription	Esophagus	oesophagus

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