Variant report

Variant	rs58879807
Chromosome Location	chr1:213135384-213135385
allele	A/C
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	POLR2A	chr1:213135337-213135388	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:213135090-213138279	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213133878..213135419-chr1:213160390..213162538,2	MCF-7	breast:

Variant related genes	Relation type
VASH2	TF binding region
ENSG00000143494	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11809007	0.94[EUR][1000 genomes]
rs17020062	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3738804	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41309631	0.87[EUR][1000 genomes]
rs41309633	0.87[EUR][1000 genomes]
rs56289940	0.82[EUR][1000 genomes]
rs58256189	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59489266	0.81[ASN][1000 genomes]
rs59676624	0.87[EUR][1000 genomes]
rs59755371	0.87[EUR][1000 genomes]
rs60620122	0.94[EUR][1000 genomes]
rs61385792	0.81[ASN][1000 genomes]
rs61583935	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832430	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832431	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832432	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832433	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832439	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73084268	0.94[EUR][1000 genomes]
rs74140537	0.94[AFR][1000 genomes]
rs7554696	0.94[EUR][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	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv11434	chr1:213131581-213156027	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213125600-213141000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:213125800-213141000	Weak transcription	A549	lung
3	chr1:213125800-213145800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:213126400-213152400	Strong transcription	Fetal Stomach	stomach
5	chr1:213126600-213140600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:213126800-213154400	Strong transcription	Fetal Brain Female	brain
7	chr1:213127000-213136400	Weak transcription	Fetal Brain Male	brain
8	chr1:213127000-213153200	Strong transcription	Fetal Lung	lung
9	chr1:213127400-213140800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:213128400-213140800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:213129000-213141600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:213129600-213139800	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr1:213130000-213153800	Weak transcription	Thymus	Thymus
14	chr1:213130600-213135600	Strong transcription	Brain Germinal Matrix	brain
15	chr1:213131200-213138000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:213131400-213139600	Weak transcription	Fetal Kidney	kidney
17	chr1:213131400-213153000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:213131600-213138600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:213131600-213139200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:213131600-213141000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:213131800-213139000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:213131800-213139200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:213131800-213140000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:213132000-213139200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:213132000-213140400	Weak transcription	Fetal Thymus	thymus
26	chr1:213132000-213141400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:213132400-213140800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:213132600-213137000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:213133000-213135400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:213133000-213139000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:213133000-213140600	Strong transcription	HSMMtube	muscle
32	chr1:213133000-213146200	Weak transcription	Esophagus	oesophagus
33	chr1:213133200-213153400	Weak transcription	Lung	lung
34	chr1:213133400-213139200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:213133400-213153800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:213133600-213135600	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:213133600-213136800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:213133600-213161600	Weak transcription	Fetal Intestine Large	intestine
39	chr1:213133800-213135400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:213133800-213138200	Genic enhancers	GM12878-XiMat	blood
41	chr1:213134200-213136600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:213134600-213152200	Weak transcription	Right Atrium	heart
43	chr1:213134800-213135800	Weak transcription	HSMM	muscle
44	chr1:213134800-213136600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:213134800-213137800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:213135000-213144800	Weak transcription	Fetal Intestine Small	intestine

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