Variant report

Variant	rs2293377
Chromosome Location	chr3:191114266-191114267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191113983..191115834-chr3:191118918..191120491,2	K562	blood:
2	chr3:191114086..191115834-chr3:191118991..191121989,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PYDC2-5	chr3:191113180-191116458	NONHSAT093967

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2293378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383437	0.86[CHD][hapmap]
rs4677732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840425	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9841435	0.88[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2293377	CCDC50	cis	Artery Tibial	GTEx
rs2293377	CCDC50	cis	Artery Aorta	GTEx
rs2293377	GP5	cis	parietal	SCAN
rs2293377	CCDC50	cis	Thyroid	GTEx
rs2293377	CCDC50	cis	Nerve Tibial	GTEx
rs2293377	CCDC50	cis	Esophagus Muscularis	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191121200	Weak transcription	Gastric	stomach
4	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
5	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
9	chr3:191094800-191114800	Weak transcription	A549	lung
10	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
13	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
17	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
18	chr3:191100200-191119600	Weak transcription	K562	blood
19	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
20	chr3:191100400-191117400	Weak transcription	Lung	lung
21	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
22	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
23	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
24	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:191101000-191115600	Weak transcription	Fetal Kidney	kidney
26	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:191101200-191115200	Weak transcription	Fetal Heart	heart
28	chr3:191101200-191115600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:191101200-191115800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:191101200-191117000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
33	chr3:191104800-191116600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:191105000-191114400	Strong transcription	Primary B cells from cord blood	blood
35	chr3:191106800-191117200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:191107200-191114400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:191107200-191114400	Strong transcription	GM12878-XiMat	blood
38	chr3:191107200-191114600	Strong transcription	HUVEC	blood vessel
39	chr3:191107400-191117200	Weak transcription	HepG2	liver
40	chr3:191108000-191117400	Weak transcription	NHEK	skin
41	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
43	chr3:191108800-191115600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:191108800-191115600	Weak transcription	Ovary	ovary
45	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
46	chr3:191109200-191117600	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:191109600-191116400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:191109800-191114400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:191110400-191115600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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