Variant report

Variant	rs11968228
Chromosome Location	chr6:56321882-56321883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17684260	1.00[AFR][1000 genomes]
rs41271874	1.00[AFR][1000 genomes]
rs45509696	1.00[AFR][1000 genomes]
rs72881014	1.00[AFR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11968228	LASS6	trans	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56309400-56322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:56313200-56322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:56313200-56323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56313800-56322200	Weak transcription	NHLF	lung
6	chr6:56314400-56323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:56315000-56322200	Weak transcription	GM12878-XiMat	blood
8	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:56315000-56349800	Strong transcription	HSMM	muscle
10	chr6:56315600-56322200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:56315800-56322000	Weak transcription	Fetal Brain Male	brain
13	chr6:56315800-56323400	Weak transcription	Aorta	Aorta
14	chr6:56315800-56329200	Weak transcription	Small Intestine	intestine
15	chr6:56316000-56323400	Weak transcription	Gastric	stomach
16	chr6:56316000-56323800	Weak transcription	Right Ventricle	heart
17	chr6:56316400-56322200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:56316400-56322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:56316400-56323800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:56316600-56322000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:56316600-56322000	Weak transcription	Psoas Muscle	Psoas
22	chr6:56316600-56323000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:56316600-56323200	Weak transcription	Ovary	ovary
24	chr6:56316600-56323200	Weak transcription	Pancreas	Pancrea
25	chr6:56316600-56323400	Weak transcription	Fetal Stomach	stomach
26	chr6:56316800-56322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:56316800-56322800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:56316800-56323600	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:56316800-56337600	Weak transcription	Hela-S3	cervix
30	chr6:56317200-56322800	Weak transcription	HepG2	liver
31	chr6:56317200-56323200	Weak transcription	Fetal Heart	heart
32	chr6:56317200-56342800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr6:56317600-56324200	Weak transcription	Brain Angular Gyrus	brain
34	chr6:56317800-56322000	Weak transcription	Brain Germinal Matrix	brain
35	chr6:56317800-56322600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:56317800-56331200	Strong transcription	HSMMtube	muscle
37	chr6:56318000-56323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:56318000-56323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:56318000-56340600	Strong transcription	Fetal Intestine Large	intestine
40	chr6:56318400-56322000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:56318400-56322000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:56318400-56322800	Weak transcription	Fetal Brain Female	brain
43	chr6:56318400-56323000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:56318600-56323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:56318600-56331000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:56318800-56325200	Strong transcription	HUVEC	blood vessel
47	chr6:56318800-56325800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:56318800-56332000	Strong transcription	Fetal Lung	lung
49	chr6:56319000-56325800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:56319000-56326000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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