Variant report

Variant	rs10242407
Chromosome Location	chr7:38875462-38875463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38873668..38876068-chr7:38880511..38882054,2	K562	blood:
2	chr7:38873915..38876598-chr7:38884159..38886331,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10085487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	0.88[EUR][1000 genomes]
rs10224856	0.81[EUR][1000 genomes]
rs10225415	0.81[EUR][1000 genomes]
rs10225550	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	1.00[ASN][1000 genomes]
rs10254354	0.81[EUR][1000 genomes]
rs10254873	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	1.00[ASN][1000 genomes]
rs10266279	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10275873	1.00[ASN][1000 genomes]
rs10951574	0.81[EUR][1000 genomes]
rs11983387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12701656	1.00[AFR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes]
rs12701671	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2040878	0.81[EUR][1000 genomes]
rs2058073	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2190667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	0.81[EUR][1000 genomes]
rs2214668	0.81[EUR][1000 genomes]
rs2215032	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2245773	0.81[EUR][1000 genomes]
rs2286089	0.81[EUR][1000 genomes]
rs2286093	0.81[EUR][1000 genomes]
rs2286101	0.81[EUR][1000 genomes]
rs2392599	0.81[EUR][1000 genomes]
rs2392608	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349310	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34358406	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[AFR][1000 genomes]
rs34886315	1.00[AFR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720300	0.81[EUR][1000 genomes]
rs4723780	0.81[EUR][1000 genomes]
rs4723781	0.81[EUR][1000 genomes]
rs4723784	0.81[EUR][1000 genomes]
rs4723787	0.81[EUR][1000 genomes]
rs6462871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462874	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	0.81[EUR][1000 genomes]
rs6951429	0.81[EUR][1000 genomes]
rs6964985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	0.81[EUR][1000 genomes]
rs6971632	1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	0.81[EUR][1000 genomes]
rs6976580	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6978805	1.00[ASN][1000 genomes]
rs6979423	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	0.81[EUR][1000 genomes]
rs7789864	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	1.00[ASN][1000 genomes]
rs7802052	0.81[EUR][1000 genomes]
rs7803488	1.00[ASN][1000 genomes]
rs9638945	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9886108	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10242407	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38863000-38876800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
9	chr7:38863800-38879600	Weak transcription	Fetal Lung	lung
10	chr7:38865800-38879600	Weak transcription	Right Atrium	heart
11	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:38866400-38876800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:38866400-38877000	Weak transcription	Primary T cells from cord blood	blood
14	chr7:38866800-38877000	Weak transcription	Primary B cells from cord blood	blood
15	chr7:38867200-38876800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:38867400-38877800	Weak transcription	Fetal Brain Male	brain
17	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
18	chr7:38867600-38879600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr7:38870000-38876600	Weak transcription	GM12878-XiMat	blood
21	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:38871000-38884400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:38871400-38880400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
27	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:38871600-38878400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:38871600-38879800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:38873200-38876800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:38873200-38884400	Weak transcription	Gastric	stomach
34	chr7:38873200-38889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
36	chr7:38874400-38878600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:38875000-38875800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:38875400-38876000	Enhancers	Pancreatic Islets	Pancreatic Islet

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