Variant report

Variant	rs2682049
Chromosome Location	chr15:56541395-56541396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
2	chr15:56540966..56543133-chr15:56718827..56720916,2	MCF-7	breast:
3	chr15:56505235..56506944-chr15:56541273..56542903,2	K562	blood:
4	chr15:56540398..56542023-chr15:56720800..56721752,16	MCF-7	breast:
5	chr15:56541012..56541917-chr15:56720826..56721341,2	K562	blood:
6	chr15:56541018..56541999-chr15:56720733..56721455,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11629483	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11631191	0.86[EUR][1000 genomes]
rs12914640	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1372753	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1829542	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2249090	0.81[AMR][1000 genomes]
rs2414464	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2460647	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2460648	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2460650	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682044	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682046	0.83[EUR][1000 genomes]
rs2682051	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682053	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682054	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713923	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2713924	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2713926	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2713931	0.82[AMR][1000 genomes]
rs2713933	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713935	0.97[ASN][1000 genomes]
rs2713936	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2713938	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2713941	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2718915	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2718941	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2725854	0.83[AMR][1000 genomes]
rs2725870	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2947021	0.81[AMR][1000 genomes]
rs35749329	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35972806	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4310791	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4310792	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59432349	0.86[EUR][1000 genomes]
rs7174823	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672886	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9672928	0.81[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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2682049	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2682049	RFX7	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56538200-56546600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:56538400-56544000	Weak transcription	Fetal Brain Male	brain
3	chr15:56538400-56546000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:56538600-56543400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:56538800-56544000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:56538800-56544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:56538800-56546400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:56538800-56546600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:56540200-56541800	Enhancers	Fetal Intestine Small	intestine
10	chr15:56540400-56541600	Enhancers	Hela-S3	cervix
11	chr15:56540600-56541400	Weak transcription	Small Intestine	intestine
12	chr15:56540600-56541400	Enhancers	Stomach Mucosa	stomach
13	chr15:56540600-56541600	Enhancers	Fetal Intestine Large	intestine
14	chr15:56540600-56543200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:56540800-56541400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr15:56540800-56544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:56541000-56541400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr15:56541000-56541400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:56541000-56541400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:56541000-56541400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr15:56541000-56541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:56541000-56541600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr15:56541000-56541600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr15:56541200-56541600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:56541200-56543000	Weak transcription	K562	blood
26	chr15:56541200-56543800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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