Variant report

Variant	rs11970960
Chromosome Location	chr7:38883838-38883839
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	chr7:38882709..38885356-chr7:38890864..38893223,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1001476	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10486680	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10951573	0.91[CEU][hapmap]
rs10951576	0.83[YRI][hapmap]
rs11971030	0.96[EUR][1000 genomes]
rs11977016	1.00[EUR][1000 genomes]
rs11978816	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11980534	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11982889	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11984145	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12112141	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13231320	0.91[CEU][hapmap]
rs1557941	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879964	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879966	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17171465	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17171466	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28680843	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34753378	0.96[EUR][1000 genomes]
rs60354841	1.00[EUR][1000 genomes]
rs6462868	0.82[YRI][hapmap]
rs68175808	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6962120	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6969435	0.90[YRI][hapmap]
rs6976100	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs713243	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73113674	0.96[EUR][1000 genomes]
rs73113680	0.96[EUR][1000 genomes]
rs73113689	0.96[EUR][1000 genomes]
rs73113699	0.96[EUR][1000 genomes]
rs73115614	0.96[EUR][1000 genomes]
rs73115622	0.96[EUR][1000 genomes]
rs73115623	0.96[EUR][1000 genomes]
rs73115628	0.96[EUR][1000 genomes]
rs73121378	0.96[EUR][1000 genomes]
rs73121380	0.96[EUR][1000 genomes]
rs73121381	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121384	0.96[EUR][1000 genomes]
rs73121386	0.96[EUR][1000 genomes]
rs73121396	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121399	1.00[EUR][1000 genomes]
rs73123603	1.00[EUR][1000 genomes]
rs73123614	1.00[EUR][1000 genomes]
rs73123618	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123621	1.00[EUR][1000 genomes]
rs73123624	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123893	0.92[EUR][1000 genomes]
rs73125633	0.92[EUR][1000 genomes]
rs7812184	1.00[CEU][hapmap];0.96[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	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
rs11970960	VPS41	Cis_1M	lymphoblastoid	RTeQTL

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

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	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
8	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
10	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:38871000-38884400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
16	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:38873200-38884400	Weak transcription	Gastric	stomach
20	chr7:38873200-38889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
22	chr7:38875800-38897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr7:38877000-38895600	Weak transcription	Spleen	Spleen
25	chr7:38877200-38888200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:38877200-38900800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:38877400-38888400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:38877400-38896200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:38878400-38888200	Weak transcription	Fetal Stomach	stomach
31	chr7:38879000-38886000	Weak transcription	Primary T cells from cord blood	blood
32	chr7:38879800-38884400	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:38879800-38891800	Weak transcription	Right Atrium	heart
34	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
35	chr7:38880000-38884400	Weak transcription	Brain Angular Gyrus	brain
36	chr7:38880000-38884400	Weak transcription	Brain Anterior Caudate	brain
37	chr7:38880000-38884400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:38880200-38885800	Weak transcription	Primary B cells from cord blood	blood
39	chr7:38880200-38897600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:38880600-38884400	Weak transcription	Ovary	ovary
41	chr7:38880600-38888200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:38880600-38888800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:38880600-38888800	Weak transcription	Lung	lung
44	chr7:38880600-38900600	Weak transcription	Adipose Nuclei	Adipose
45	chr7:38880800-38888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:38881200-38884800	Weak transcription	Small Intestine	intestine
48	chr7:38881200-38888800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:38881200-38888800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:38881200-38895000	Weak transcription	GM12878-XiMat	blood

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