Variant report

Variant	rs3740768
Chromosome Location	chr11:76669891-76669892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDPD4-2	chr11:76669878-76670057	ENSG00000254988.1

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10899314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236997	0.81[EUR][1000 genomes]
rs11237030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11605656	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606034	0.80[EUR][1000 genomes]
rs11606467	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12223477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12797827	0.83[ASN][1000 genomes]
rs17812687	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1945084	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1945085	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2048954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2187499	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2372387	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3740766	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862808	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4016126	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944130	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944133	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4945128	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55743360	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55798841	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55977032	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56129156	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56789915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61895512	0.80[EUR][1000 genomes]
rs61900090	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61900119	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61900120	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7118398	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519700	chr11:76637651-76709407	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1042924	chr11:76659477-76709407	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1040833	chr11:76667160-76709407	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76631400-76688400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:76631600-76670200	Weak transcription	Left Ventricle	heart
3	chr11:76631600-76671600	Weak transcription	Ovary	ovary
4	chr11:76645800-76683800	Weak transcription	Esophagus	oesophagus
5	chr11:76646200-76670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:76646600-76688000	Weak transcription	HMEC	breast
7	chr11:76647000-76670200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:76647200-76671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:76647200-76673800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:76647200-76674800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:76647400-76670000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:76648400-76671600	Weak transcription	Spleen	Spleen
13	chr11:76649600-76672000	Weak transcription	Aorta	Aorta
14	chr11:76650600-76670000	Weak transcription	Placenta	Placenta
15	chr11:76650600-76681200	Weak transcription	Brain Substantia Nigra	brain
16	chr11:76655800-76671600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:76655800-76674200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:76655800-76681800	Weak transcription	Primary B cells from cord blood	blood
19	chr11:76656200-76677000	Weak transcription	Brain Anterior Caudate	brain
20	chr11:76656400-76671200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:76656800-76670000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:76657000-76670200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:76657000-76674600	Weak transcription	Fetal Stomach	stomach
24	chr11:76657000-76676600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:76657200-76688400	Weak transcription	Gastric	stomach
26	chr11:76657400-76670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:76657600-76671600	Weak transcription	Lung	lung
28	chr11:76657600-76672600	Weak transcription	Brain Germinal Matrix	brain
29	chr11:76659600-76673600	Weak transcription	Small Intestine	intestine
30	chr11:76659800-76673400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:76659800-76673600	Weak transcription	Primary T cells from cord blood	blood
32	chr11:76660000-76710800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:76660200-76672800	Weak transcription	Fetal Intestine Small	intestine
34	chr11:76661200-76673800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:76661200-76674600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:76661800-76673400	Weak transcription	Pancreas	Pancrea
37	chr11:76662000-76671400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:76662800-76673600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:76663000-76671600	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:76663000-76674600	Weak transcription	Liver	Liver
41	chr11:76664200-76673200	Weak transcription	Fetal Intestine Large	intestine
42	chr11:76665200-76673400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:76665800-76688400	Weak transcription	Right Ventricle	heart
44	chr11:76666800-76671600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:76666800-76671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:76666800-76673600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:76666800-76677600	Weak transcription	Hela-S3	cervix
48	chr11:76666800-76695400	Weak transcription	NHEK	skin
49	chr11:76667400-76673800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:76667600-76673400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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