Variant report

Variant	rs6930960
Chromosome Location	chr6:33850985-33850986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITPR3-4	chr6:33850947-33851188	NONHSAT109687

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16869648	0.82[EUR][1000 genomes]
rs16869660	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs58823120	0.86[EUR][1000 genomes]
rs58937462	0.86[EUR][1000 genomes]
rs6918090	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6926599	1.00[EUR][1000 genomes]
rs73416177	0.82[EUR][1000 genomes]
rs73416178	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73418511	0.87[EUR][1000 genomes]
rs73418515	1.00[EUR][1000 genomes]
rs744686	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs744687	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs744688	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7746977	0.81[EUR][1000 genomes]
rs7748471	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7748483	1.00[CEU][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7767294	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7767496	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6930960	HLA-DPB1	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33844200-33852600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:33847200-33852000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:33847600-33852600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:33848200-33852800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:33848200-33853000	Weak transcription	Colonic Mucosa	Colon
6	chr6:33849200-33852000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:33849400-33851000	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr6:33850000-33860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:33850000-33871800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33850200-33852600	Weak transcription	Esophagus	oesophagus
11	chr6:33850200-33853600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:33850400-33851200	Weak transcription	Fetal Intestine Large	intestine
13	chr6:33850400-33852400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:33850400-33852400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:33850400-33852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:33850400-33852800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:33850400-33852800	Weak transcription	NHEK	skin
18	chr6:33850400-33853200	Weak transcription	Left Ventricle	heart
19	chr6:33850400-33853200	Weak transcription	Right Atrium	heart
20	chr6:33850400-33853200	Weak transcription	Right Ventricle	heart
21	chr6:33850400-33853800	Weak transcription	Fetal Lung	lung
22	chr6:33850600-33852200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:33850600-33852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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