Variant report

Variant	rs62179068
Chromosome Location	chr2:180138126-180138127
allele	A/G
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	BRCA1	chr2:180137670-180138158	Hela-S3	cervix:	n/a	n/a
2	MBD4	chr2:180136817-180138430	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:180137214-180138930	HepG2	liver:	n/a	n/a
4	NFIC	chr2:180136699-180138163	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
2	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237477	TF binding region
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12622222	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17363057	1.00[AFR][1000 genomes]
rs17454087	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17454199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17454527	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62175447	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs62175448	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62175449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62175450	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177277	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177281	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177283	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62177285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177287	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177289	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62177291	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62177326	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62177327	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62177328	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62177330	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62177332	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177335	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177336	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177337	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177338	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177339	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179066	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179067	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179069	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180138200	Weak transcription	Aorta	Aorta
2	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:180130600-180138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:180133600-180138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:180133600-180138800	Weak transcription	Placenta	Placenta
9	chr2:180133600-180140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:180133800-180138800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:180133800-180138800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:180133800-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:180133800-180141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:180134000-180139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:180134000-180142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:180135000-180138200	Enhancers	Brain Hippocampus Middle	brain
17	chr2:180135200-180140400	Enhancers	Brain Angular Gyrus	brain
18	chr2:180135400-180140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:180136200-180138200	Enhancers	HUVEC	blood vessel
20	chr2:180136200-180138200	Enhancers	NHEK	skin
21	chr2:180136600-180141000	Weak transcription	Esophagus	oesophagus
22	chr2:180136800-180138800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:180137000-180139000	Flanking Active TSS	HepG2	liver
24	chr2:180137000-180139600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:180137000-180140600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr2:180137200-180138200	Flanking Active TSS	Hela-S3	cervix
27	chr2:180137200-180138600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:180137200-180138800	Enhancers	Fetal Lung	lung
29	chr2:180137200-180140000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:180137200-180141200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:180137200-180141200	Enhancers	Adipose Nuclei	Adipose
32	chr2:180137400-180138200	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:180137400-180138200	Enhancers	Fetal Intestine Large	intestine
34	chr2:180137400-180138400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:180137400-180138600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:180137400-180138800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:180137400-180138800	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr2:180137400-180140400	Enhancers	Brain Anterior Caudate	brain
39	chr2:180137400-180141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:180137400-180141200	Enhancers	Fetal Stomach	stomach
41	chr2:180137600-180138800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:180137600-180140600	Weak transcription	Stomach Mucosa	stomach
43	chr2:180137600-180141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:180137800-180138400	Weak transcription	A549	lung
45	chr2:180137800-180138600	Enhancers	Fetal Muscle Leg	muscle
46	chr2:180137800-180138600	Enhancers	HMEC	breast
47	chr2:180137800-180138600	Enhancers	HSMMtube	muscle
48	chr2:180137800-180138800	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr2:180137800-180139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:180137800-180140400	Weak transcription	Duodenum Mucosa	Duodenum

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