Variant report

Variant	rs7558427
Chromosome Location	chr2:85986112-85986113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85968240..85969762-chr2:85984026..85986176,2	MCF-7	breast:
2	chr2:85820402..85822148-chr2:85985989..85987607,2	K562	blood:
3	chr2:85980194..85982754-chr2:85983274..85986188,2	MCF-7	breast:
4	chr2:85978299..85982143-chr2:85985219..85987371,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATOH8-3	chr2:85985442-85986185	l_1877_chr2:85969788-85975170_thyroid

Variant related genes	Relation type
ENSG00000168874	Chromatin interaction

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

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

rs_ID	r²[population]
rs12475263	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13013824	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832009	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4832193	0.83[GIH][hapmap]
rs4832195	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832196	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719105	0.87[ASN][1000 genomes]
rs6746541	0.83[CHB][hapmap];0.94[JPT][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	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85983000-85990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:85983400-85987000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr2:85983400-85987000	Transcr. at gene 5' and 3'	HSMM	muscle
4	chr2:85983600-85987000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr2:85983600-85989000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:85983600-85989200	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr2:85983800-85986400	Enhancers	Brain Angular Gyrus	brain
8	chr2:85983800-85986600	Genic enhancers	Gastric	stomach
9	chr2:85984000-85986600	Genic enhancers	Spleen	Spleen
10	chr2:85984200-85986200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:85984200-85987000	Weak transcription	NH-A	brain
12	chr2:85984200-85992000	Weak transcription	Fetal Kidney	kidney
13	chr2:85984400-85986400	Enhancers	Brain Substantia Nigra	brain
14	chr2:85984400-85986600	Genic enhancers	Lung	lung
15	chr2:85984400-85987400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:85984400-85988000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:85984400-85988000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:85984400-85988000	Genic enhancers	Ovary	ovary
19	chr2:85984400-85988000	Weak transcription	HSMMtube	muscle
20	chr2:85984400-85988200	Enhancers	Brain Hippocampus Middle	brain
21	chr2:85984600-85987000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:85984600-85987600	Weak transcription	A549	lung
23	chr2:85984600-85987800	Weak transcription	HUVEC	blood vessel
24	chr2:85984600-85988000	Weak transcription	Fetal Heart	heart
25	chr2:85984600-85988000	Weak transcription	Fetal Intestine Large	intestine
26	chr2:85984600-85990200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:85984800-85986800	Genic enhancers	Right Ventricle	heart
28	chr2:85985200-85986400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr2:85985200-85986600	Bivalent Enhancer	Placenta	Placenta
30	chr2:85985200-85989200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:85985400-85986600	Genic enhancers	Aorta	Aorta
32	chr2:85985400-85986600	Genic enhancers	Pancreas	Pancrea
33	chr2:85985400-85986600	Flanking Active TSS	Right Atrium	heart
34	chr2:85985400-85986600	Genic enhancers	NHLF	lung
35	chr2:85985400-85987000	Enhancers	Brain Germinal Matrix	brain
36	chr2:85985400-85987000	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:85985400-85995200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:85985600-85987000	Genic enhancers	Brain Anterior Caudate	brain
39	chr2:85985600-85987000	Enhancers	Psoas Muscle	Psoas
40	chr2:85985600-85987200	Enhancers	Colonic Mucosa	Colon
41	chr2:85985600-85987600	Strong transcription	Osteobl	bone
42	chr2:85985800-85986200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:85985800-85986200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:85985800-85986200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr2:85985800-85986600	Enhancers	Esophagus	oesophagus
46	chr2:85985800-85987000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:85985800-85987000	Enhancers	HepG2	liver
48	chr2:85985800-85987000	Weak transcription	NHDF-Ad	bronchial
49	chr2:85985800-85988200	Weak transcription	Stomach Mucosa	stomach
50	chr2:85986000-85986200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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