Variant report

Variant	rs3798734
Chromosome Location	chr6:11201157-11201158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf228-2	chr6:11200607-11201794	ENSG00000249190

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10807059	0.90[EUR][1000 genomes]
rs10947017	0.92[EUR][1000 genomes]
rs10947020	0.83[EUR][1000 genomes]
rs10947021	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs10947026	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs12190771	0.94[CEU][hapmap]
rs12190858	0.92[EUR][1000 genomes]
rs12205037	0.85[EUR][1000 genomes]
rs12215094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12215491	0.89[CEU][hapmap]
rs2034	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327332	0.89[CEU][hapmap]
rs3102	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3756966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778170	0.92[EUR][1000 genomes]
rs3778171	0.92[EUR][1000 genomes]
rs3798733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3798736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798737	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs3798738	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3798740	0.81[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798743	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6912916	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6915811	0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6928520	0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6937575	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs726230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729747	0.82[CEU][hapmap]
rs9295813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798734	NEDD9	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11179000-11202200	Weak transcription	Brain Substantia Nigra	brain
2	chr6:11185800-11202600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:11190800-11201400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:11191800-11201400	Weak transcription	Esophagus	oesophagus
5	chr6:11192000-11202600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:11192800-11202800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:11192800-11207000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:11192800-11207200	Weak transcription	Liver	Liver
9	chr6:11194000-11202200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:11194000-11202600	Weak transcription	Brain Germinal Matrix	brain
11	chr6:11195000-11203200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:11195400-11201400	Weak transcription	Gastric	stomach
13	chr6:11195400-11203200	Enhancers	Thymus	Thymus
14	chr6:11195400-11207200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:11195600-11202200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:11195600-11207400	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:11196000-11202000	Weak transcription	Stomach Mucosa	stomach
18	chr6:11196000-11203000	Weak transcription	Psoas Muscle	Psoas
19	chr6:11196200-11201600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:11196600-11201800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr6:11196800-11201800	Genic enhancers	Left Ventricle	heart
22	chr6:11197000-11211000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:11197000-11211200	Genic enhancers	HepG2	liver
24	chr6:11197400-11204000	Enhancers	NHDF-Ad	bronchial
25	chr6:11197600-11201400	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:11197800-11202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:11197800-11203200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:11197800-11204600	Strong transcription	Primary B cells from cord blood	blood
29	chr6:11198000-11201200	Weak transcription	Brain Anterior Caudate	brain
30	chr6:11198000-11201600	Strong transcription	Fetal Intestine Small	intestine
31	chr6:11198000-11202200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:11198200-11202200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:11198200-11207000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:11198400-11201200	Weak transcription	Fetal Brain Female	brain
35	chr6:11198400-11201400	Weak transcription	Fetal Lung	lung
36	chr6:11198400-11201600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:11198400-11201600	Strong transcription	Fetal Stomach	stomach
38	chr6:11198400-11202800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:11198400-11203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:11198400-11203000	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:11198400-11203800	Genic enhancers	Osteobl	bone
42	chr6:11198400-11206600	Genic enhancers	A549	lung
43	chr6:11198600-11202200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:11198600-11203600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:11198800-11201200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:11198800-11201400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:11198800-11202000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:11198800-11202600	Enhancers	Primary hematopoietic stem cells	blood
49	chr6:11198800-11205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:11199000-11201200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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