Variant report

Variant	rs529523
Chromosome Location	chr3:191110320-191110321
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	chr3:191109601..191112408-chr3:191114470..191116944,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10937477	0.89[ASN][1000 genomes]
rs13061649	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1347400	0.87[ASN][1000 genomes]
rs1465737	0.86[EUR][1000 genomes]
rs1473866	0.89[ASN][1000 genomes]
rs150506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159488	0.87[ASN][1000 genomes]
rs159489	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656143	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1662184	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs167148	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176820	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176821	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176822	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs184140	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186064	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186065	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186066	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188384	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188385	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs192671	0.81[ASN][1000 genomes]
rs211043	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2572064	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293797	0.91[ASN][1000 genomes]
rs293798	0.89[ASN][1000 genomes]
rs293800	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293802	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293804	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293805	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293806	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293807	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293808	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293809	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293810	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293811	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293812	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293813	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293814	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293815	0.91[ASN][1000 genomes]
rs293837	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293839	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293840	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293841	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293844	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293846	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293851	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297396	0.91[ASN][1000 genomes]
rs364519	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs366626	0.93[ASN][1000 genomes]
rs367747	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368665	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373035	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381090	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383529	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs386241	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs389765	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs390744	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392311	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs399575	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs401465	0.91[ASN][1000 genomes]
rs403078	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs407226	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs415149	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs420266	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs426466	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429374	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs429521	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs432085	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436393	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs436428	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs437244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438589	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs441509	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs445914	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs447931	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs448133	0.91[ASN][1000 genomes]
rs449398	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4677630	0.87[ASN][1000 genomes]
rs4677734	0.87[ASN][1000 genomes]
rs4677735	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491252	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs513632	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs520494	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs520600	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs523270	0.91[ASN][1000 genomes]
rs525774	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526785	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566548	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568702	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs578401	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6779820	0.87[ASN][1000 genomes]
rs6953	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697905	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709142	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847278	0.85[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs529523	CCDC50	cis	Thyroid	GTEx
rs529523	CCDC50	cis	Artery Aorta	GTEx
rs529523	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:191079600-191121200	Weak transcription	Gastric	stomach
5	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
6	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
11	chr3:191094800-191114800	Weak transcription	A549	lung
12	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:191098000-191111400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
16	chr3:191099600-191113800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:191099600-191114000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
22	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
23	chr3:191100200-191119600	Weak transcription	K562	blood
24	chr3:191100400-191114000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
26	chr3:191100400-191117400	Weak transcription	Lung	lung
27	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
28	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
29	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
30	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:191101000-191115600	Weak transcription	Fetal Kidney	kidney
32	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:191101200-191113600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:191101200-191114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:191101200-191115200	Weak transcription	Fetal Heart	heart
36	chr3:191101200-191115600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:191101200-191115800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:191101200-191117000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:191102200-191117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:191102400-191110800	Weak transcription	Fetal Lung	lung
41	chr3:191102800-191113400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
43	chr3:191104800-191116600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:191105000-191110800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:191105000-191114400	Strong transcription	Primary B cells from cord blood	blood
46	chr3:191106000-191110800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:191106800-191117200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:191107000-191110400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:191107000-191110600	Strong transcription	Fetal Intestine Large	intestine
50	chr3:191107000-191111200	Strong transcription	Adipose Nuclei	Adipose

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