Variant report

Variant	rs293804
Chromosome Location	chr3:191090773-191090774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191089153..191091755-chr3:191092405..191093970,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PYDC2-7	chr3:191089936-191090896	NONHSAT093966

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10937477	0.87[ASN][1000 genomes]
rs13061649	0.81[EUR][1000 genomes]
rs1347400	0.85[ASN][1000 genomes]
rs1465737	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1473866	0.87[ASN][1000 genomes]
rs150506	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159488	0.85[ASN][1000 genomes]
rs159489	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662184	0.81[EUR][1000 genomes]
rs167148	0.81[EUR][1000 genomes]
rs176820	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176821	0.81[EUR][1000 genomes]
rs176822	0.81[EUR][1000 genomes]
rs184140	0.81[EUR][1000 genomes]
rs186064	0.81[EUR][1000 genomes]
rs186065	0.81[EUR][1000 genomes]
rs186066	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs188384	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188385	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211043	0.81[EUR][1000 genomes]
rs293797	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs293798	0.87[ASN][1000 genomes]
rs293800	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293802	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293805	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293806	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293807	0.81[EUR][1000 genomes]
rs293808	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293809	0.81[EUR][1000 genomes]
rs293810	0.81[EUR][1000 genomes]
rs293811	0.81[EUR][1000 genomes]
rs293812	0.81[EUR][1000 genomes]
rs293813	0.81[EUR][1000 genomes]
rs293814	0.81[EUR][1000 genomes]
rs293815	0.89[ASN][1000 genomes]
rs293844	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293846	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293851	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297396	0.89[ASN][1000 genomes]
rs364519	0.81[EUR][1000 genomes]
rs366626	0.91[ASN][1000 genomes]
rs367747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368665	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369174	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373035	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381090	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383075	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383529	0.81[EUR][1000 genomes]
rs389765	0.81[EUR][1000 genomes]
rs390744	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401465	0.89[ASN][1000 genomes]
rs403078	0.81[EUR][1000 genomes]
rs407226	0.81[EUR][1000 genomes]
rs415149	0.81[EUR][1000 genomes]
rs426466	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429374	0.81[EUR][1000 genomes]
rs432085	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437244	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441509	0.81[EUR][1000 genomes]
rs445914	0.81[EUR][1000 genomes]
rs448133	0.89[ASN][1000 genomes]
rs449398	0.81[EUR][1000 genomes]
rs4677630	0.85[ASN][1000 genomes]
rs4677734	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4677735	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523270	0.89[ASN][1000 genomes]
rs525774	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs526785	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529523	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566548	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578401	0.81[EUR][1000 genomes]
rs6779820	0.85[ASN][1000 genomes]
rs6953	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697905	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709142	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847278	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv592852	chr3:191073228-191093310	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv592853	chr3:191073228-191094985	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs293804	CCDC50	cis	Artery Aorta	GTEx
rs293804	CCDC50	cis	Artery Tibial	GTEx
rs293804	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
3	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
4	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
8	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:191074800-191094200	Weak transcription	A549	lung
10	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
11	chr3:191076000-191092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:191076200-191091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:191077600-191094200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:191079400-191093000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:191079400-191094200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:191079400-191094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:191079600-191092600	Weak transcription	Primary T cells from cord blood	blood
19	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
20	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:191079600-191121200	Weak transcription	Gastric	stomach
22	chr3:191079800-191094200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:191080200-191094600	Weak transcription	Stomach Mucosa	stomach
24	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
26	chr3:191080400-191092800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:191080600-191092800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:191080600-191094200	Weak transcription	Right Ventricle	heart
29	chr3:191080600-191094400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:191081600-191094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:191081800-191092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:191082200-191092800	Weak transcription	Aorta	Aorta
34	chr3:191082400-191092800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:191083000-191094800	Strong transcription	Liver	Liver
36	chr3:191083400-191092800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:191084200-191094200	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:191085000-191092600	Weak transcription	NHLF	lung
39	chr3:191085000-191096000	Weak transcription	K562	blood
40	chr3:191085800-191093800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:191087400-191093200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:191087800-191092800	Weak transcription	HSMM	muscle
44	chr3:191087800-191093000	Weak transcription	HSMMtube	muscle
45	chr3:191087800-191093800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:191087800-191100000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:191088000-191092400	Weak transcription	NHDF-Ad	bronchial
49	chr3:191088000-191092800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:191088000-191092800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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