Variant report

Variant	rs6563646
Chromosome Location	chr13:39443513-39443514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39442388..39444507-chr13:39446931..39448691,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11616774	0.83[EUR][1000 genomes]
rs11618539	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1540131	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894105	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1945502	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1945511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226913	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146172	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4943613	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945502	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6563647	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7324518	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548465	0.83[CEU][hapmap]
rs9548509	0.84[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv983708	chr13:39443415-39445775	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39416200-39450200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:39419000-39449800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:39419200-39452600	Weak transcription	Fetal Intestine Large	intestine
4	chr13:39420800-39454600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:39424200-39457800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:39424800-39449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr13:39430600-39458000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:39430600-39462400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:39432200-39458200	Weak transcription	Gastric	stomach
10	chr13:39432600-39468600	Weak transcription	Psoas Muscle	Psoas
11	chr13:39433800-39451000	Weak transcription	Fetal Kidney	kidney
12	chr13:39433800-39456600	Weak transcription	Fetal Stomach	stomach
13	chr13:39434400-39446200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:39434800-39448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:39436000-39445200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:39436000-39457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr13:39438800-39445200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:39438800-39450000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:39441200-39444600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:39442600-39443600	Enhancers	Liver	Liver
21	chr13:39443000-39448400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:39443200-39450200	Weak transcription	Pancreas	Pancrea
23	chr13:39443400-39448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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