Variant report

Variant	rs4723780
Chromosome Location	chr7:38770597-38770598
allele	A/T
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	JUN	chr7:38770454-38770629	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38767860..38770728-chr7:38772914..38774538,2	MCF-7	breast:

Variant related genes	Relation type
VPS41	TF binding region

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10085487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1012976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225550	1.00[CHB][hapmap]
rs10229055	1.00[CHB][hapmap]
rs10242407	0.81[EUR][1000 genomes]
rs10254354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs12112381	0.87[YRI][hapmap]
rs12701653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701656	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs13224619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224857	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229445	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13231372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs13235997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	0.81[EUR][1000 genomes]
rs13238093	0.80[EUR][1000 genomes]
rs1558111	1.00[CHB][hapmap]
rs17240051	1.00[ASN][1000 genomes]
rs17680342	1.00[CEU][hapmap]
rs2040878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058073	0.85[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2108508	0.81[EUR][1000 genomes]
rs2189854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190667	1.00[CHB][hapmap]
rs2190668	0.81[EUR][1000 genomes]
rs2190670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2214667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286103	1.00[JPT][hapmap]
rs2392599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392608	1.00[CHB][hapmap]
rs2392610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34349310	0.80[EUR][1000 genomes]
rs34358406	0.80[EUR][1000 genomes]
rs34621392	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997080	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35220172	1.00[ASN][1000 genomes]
rs35400125	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632362	0.80[EUR][1000 genomes]
rs35667896	0.91[EUR][1000 genomes]
rs35816439	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843038	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	0.91[EUR][1000 genomes]
rs36114334	0.94[EUR][1000 genomes]
rs36121032	0.81[EUR][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs40445	0.81[EUR][1000 genomes]
rs4720300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723786	1.00[JPT][hapmap]
rs4723787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723802	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723804	1.00[ASN][1000 genomes]
rs57617719	0.86[AFR][1000 genomes]
rs58454657	0.89[AFR][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462873	1.00[CHB][hapmap]
rs6947695	1.00[CHB][hapmap]
rs6949958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6963090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6967384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971632	1.00[CHB][hapmap]
rs6975410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap]
rs6979423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71548633	0.83[EUR][1000 genomes]
rs73370730	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757685	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	1.00[ASN][1000 genomes]
rs7782140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7782277	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7787423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7793250	1.00[CHB][hapmap]
rs7799887	1.00[CHB][hapmap]
rs7802052	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802623	0.89[AFR][1000 genomes]
rs7803488	1.00[CHB][hapmap]
rs9638945	1.00[CHB][hapmap]
rs976350	1.00[JPT][hapmap]
rs976352	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4723780	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38757000-38784200	Weak transcription	HMEC	breast
5	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
6	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
8	chr7:38759000-38770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:38759200-38810200	Weak transcription	A549	lung
10	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
12	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
16	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
18	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
20	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:38763400-38780400	Weak transcription	Fetal Kidney	kidney
22	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
23	chr7:38763400-38828800	Weak transcription	HepG2	liver
24	chr7:38763600-38772000	Strong transcription	Liver	Liver
25	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:38764200-38772000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr7:38764200-38772800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:38764400-38771800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:38764400-38787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:38764800-38775000	Weak transcription	Fetal Heart	heart
31	chr7:38764800-38775200	Weak transcription	HSMMtube	muscle
32	chr7:38764800-38784200	Weak transcription	NHEK	skin
33	chr7:38765400-38784200	Weak transcription	NHLF	lung
34	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:38765600-38779600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:38765600-38779600	Weak transcription	Spleen	Spleen
38	chr7:38765600-38784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:38765600-38784400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:38766000-38784200	Weak transcription	NH-A	brain
41	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:38766200-38780000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:38766200-38783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:38766600-38780600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:38766600-38782600	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:38766800-38772800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:38766800-38784200	Weak transcription	NHDF-Ad	bronchial
49	chr7:38767000-38779200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:38767200-38771000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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