Variant report

Variant	rs16987880
Chromosome Location	chr2:20799837-20799838
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:1)
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	chr2:20785689..20787635-chr2:20799308..20801529,2	K562	blood:
4	chr2:20798546..20802204-chr2:20815122..20819483,4	MCF-7	breast:
5	chr2:20794523..20801165-chr2:20801395..20807064,11	K562	blood:
6	chr2:20798603..20801119-chr2:20825014..20826613,2	K562	blood:
7	chr2:20798617..20801050-chr2:20836301..20838004,2	MCF-7	breast:
8	chr2:20674472..20676562-chr2:20797774..20800276,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDF7-4	chr2:20799440-20799918	NONHSAT069453

No data

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

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10166792	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10177787	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10190705	0.84[ASN][1000 genomes]
rs10195324	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10195722	0.93[JPT][hapmap]
rs10200207	0.83[ASN][1000 genomes]
rs11096677	0.88[ASN][1000 genomes]
rs11096679	0.81[JPT][hapmap]
rs1123781	0.89[ASN][1000 genomes]
rs11691255	0.84[ASN][1000 genomes]
rs11885969	0.81[JPT][hapmap]
rs12472478	0.93[JPT][hapmap]
rs12621527	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs13013281	0.81[JPT][hapmap]
rs13031724	0.81[JPT][hapmap]
rs13422371	0.84[ASN][1000 genomes]
rs16987857	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16987878	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	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2882036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666315	0.89[CEU][hapmap];0.88[ASN][1000 genomes]
rs4666429	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4666430	0.93[JPT][hapmap]
rs4666431	0.93[JPT][hapmap]
rs4666436	0.81[JPT][hapmap]
rs55835545	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56129345	0.94[ASN][1000 genomes]
rs59169527	0.95[ASN][1000 genomes]
rs72782365	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72782367	0.99[ASN][1000 genomes]
rs72782368	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766474	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs921601	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
2	chr2:20789200-20800400	Enhancers	Placenta	Placenta
3	chr2:20790800-20801200	Enhancers	Adipose Nuclei	Adipose
4	chr2:20791800-20800400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:20792400-20800200	Enhancers	Right Atrium	heart
6	chr2:20792800-20801800	Enhancers	HUVEC	blood vessel
7	chr2:20793000-20800400	Enhancers	Left Ventricle	heart
8	chr2:20793000-20801200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:20793800-20801400	Enhancers	Brain Angular Gyrus	brain
10	chr2:20794200-20800000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:20794600-20800200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:20794800-20801200	Enhancers	Brain Anterior Caudate	brain
13	chr2:20794800-20801200	Enhancers	Brain Substantia Nigra	brain
14	chr2:20795000-20801200	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:20795000-20801600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:20795000-20802000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:20795600-20800000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:20795600-20800200	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:20795600-20800200	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:20795800-20801000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:20796000-20800000	Enhancers	Fetal Brain Male	brain
22	chr2:20796000-20802400	Weak transcription	NHEK	skin
23	chr2:20796200-20804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:20796600-20804400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:20796800-20800600	Enhancers	Liver	Liver
26	chr2:20797000-20803800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:20797000-20810600	Weak transcription	Colonic Mucosa	Colon
28	chr2:20797600-20810600	Weak transcription	Fetal Kidney	kidney
29	chr2:20797800-20804000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:20797800-20804400	Weak transcription	Fetal Lung	lung
31	chr2:20797800-20804400	Weak transcription	NH-A	brain
32	chr2:20797800-20804400	Weak transcription	NHLF	lung
33	chr2:20797800-20810800	Weak transcription	Gastric	stomach
34	chr2:20798000-20801200	Enhancers	HepG2	liver
35	chr2:20798000-20802600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:20798200-20800800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:20798200-20802400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:20798200-20804200	Weak transcription	Ovary	ovary
39	chr2:20798400-20800000	Enhancers	Fetal Muscle Leg	muscle
40	chr2:20798400-20800400	Enhancers	Lung	lung
41	chr2:20798400-20801200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr2:20798600-20800400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:20798800-20800000	Enhancers	Aorta	Aorta
44	chr2:20798800-20800000	Enhancers	Colon Smooth Muscle	Colon
45	chr2:20798800-20800200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:20798800-20800200	Enhancers	Pancreas	Pancrea
47	chr2:20798800-20800400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:20798800-20800400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:20798800-20800400	Enhancers	NHDF-Ad	bronchial
50	chr2:20798800-20801000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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