Variant report

Variant	rs2682044
Chromosome Location	chr15:56503808-56503809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56502619..56504153-chr15:56505058..56507337,2	MCF-7	breast:
2	chr15:56503289..56505951-chr15:56511015..56513534,2	K562	blood:
3	chr15:56499669..56501343-chr15:56501763..56504338,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11629483	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905899	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907263	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911094	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12911427	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12914640	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372753	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442640	0.82[EUR][1000 genomes]
rs1829542	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119937	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2414464	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460647	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460650	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682046	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682049	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682051	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682053	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682054	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2713923	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713924	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713933	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2713936	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713938	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713941	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718915	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718941	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725854	0.81[AMR][1000 genomes]
rs2725870	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34044869	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34144128	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34224072	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34386737	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34756325	0.88[ASN][1000 genomes]
rs35082998	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35749329	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35972806	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310791	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310792	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774232	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774847	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774848	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59432349	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044082	0.81[ASN][1000 genomes]
rs62044110	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165270	0.81[EUR][1000 genomes]
rs7168319	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175745	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7496025	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024031	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028353	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029114	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033653	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9672886	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672928	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[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	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	nsv528965	chr15:56489159-56504598	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2682044	RFX7	cis	Adipose Subcutaneous	GTEx
rs2682044	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
3	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
5	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
6	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:56493200-56515400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:56495200-56504400	Weak transcription	Fetal Intestine Large	intestine
9	chr15:56496600-56515200	Weak transcription	Left Ventricle	heart
10	chr15:56497400-56505000	Weak transcription	HSMMtube	muscle
11	chr15:56498200-56508000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:56498400-56504400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:56498400-56514400	Weak transcription	NHEK	skin
14	chr15:56498400-56515200	Weak transcription	HUVEC	blood vessel
15	chr15:56500200-56504000	Weak transcription	A549	lung
16	chr15:56500600-56513000	Weak transcription	HMEC	breast
17	chr15:56500600-56515200	Weak transcription	Ovary	ovary
18	chr15:56500800-56504000	Weak transcription	NHDF-Ad	bronchial
19	chr15:56500800-56507600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:56500800-56508000	Weak transcription	Right Ventricle	heart
21	chr15:56500800-56514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:56500800-56515200	Weak transcription	Thymus	Thymus
23	chr15:56501000-56504400	Weak transcription	HSMM	muscle
24	chr15:56501400-56504400	Weak transcription	K562	blood
25	chr15:56501400-56507800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:56501400-56508000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:56501600-56507600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:56501600-56508400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:56501600-56511800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:56501800-56504000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:56501800-56505800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:56502000-56504400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:56502000-56506400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:56502000-56507600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:56502000-56507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:56502200-56508400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:56502400-56514600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:56502600-56505800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr15:56502600-56506000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:56502600-56507600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:56502800-56504000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:56502800-56508000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:56503000-56505800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:56503200-56504000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr15:56503200-56505000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:56503200-56505400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr15:56503200-56506400	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr15:56503400-56504000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:56503400-56504200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:56503400-56506400	ZNF genes & repeats	Primary B cells from cord blood	blood

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