Variant report

Variant	rs11542549
Chromosome Location	chr3:191075902-191075903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:191075600-191076480	PFSK-1	brain:	n/a	n/a
2	CEBPB	chr3:191075765-191076112	H1-hESC	embryonic stem cell:	n/a	n/a
3	WRNIP1	chr3:191075566-191075930	GM12878	blood:	n/a	n/a
4	JUND	chr3:191075823-191076071	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191049298..191052407-chr3:191074621..191077632,4	K562	blood:
2	chr3:191049478..191053328-chr3:191074760..191077632,3	K562	blood:

Variant related genes	Relation type
CCDC50	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1435062	0.93[ASN][1000 genomes]
rs1473869	0.92[ASN][1000 genomes]
rs1520202	0.89[ASN][1000 genomes]
rs1520203	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1609926	0.90[ASN][1000 genomes]
rs16822378	0.90[ASN][1000 genomes]
rs16822382	0.90[ASN][1000 genomes]
rs16866487	0.92[ASN][1000 genomes]
rs16866504	0.95[ASN][1000 genomes]
rs16866505	0.95[ASN][1000 genomes]
rs17753967	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17810246	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17810282	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17838893	0.92[ASN][1000 genomes]
rs2056333	0.92[ASN][1000 genomes]
rs2364379	0.96[ASN][1000 genomes]
rs28715898	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796219	0.89[ASN][1000 genomes]
rs3959143	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4677631	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677632	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677725	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677726	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677727	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56174842	0.92[ASN][1000 genomes]
rs57211729	0.96[ASN][1000 genomes]
rs58141749	0.91[ASN][1000 genomes]
rs58645265	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59709586	0.87[ASN][1000 genomes]
rs61250936	0.85[ASN][1000 genomes]
rs6444541	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73185209	0.95[ASN][1000 genomes]
rs73185210	0.97[ASN][1000 genomes]
rs73185213	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185226	0.95[ASN][1000 genomes]
rs73185228	0.93[ASN][1000 genomes]
rs73185240	0.91[ASN][1000 genomes]
rs73185255	0.91[ASN][1000 genomes]
rs73185263	0.90[ASN][1000 genomes]
rs73185284	0.86[ASN][1000 genomes]
rs73185287	0.86[ASN][1000 genomes]
rs73185288	0.84[ASN][1000 genomes]
rs73201627	0.89[ASN][1000 genomes]
rs73201628	0.89[ASN][1000 genomes]
rs73201630	0.89[ASN][1000 genomes]
rs73201631	0.89[ASN][1000 genomes]
rs7637196	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642387	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7648886	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9290986	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823680	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824437	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9839751	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9843934	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853569	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9863255	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv508266	chr3:191064212-191083637	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1808657	chr3:191064330-191081793	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv878106	chr3:191064528-191081344	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1823184	chr3:191064803-191082303	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1848120	chr3:191064803-191082303	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11542549	CCDC50	cis	Artery Tibial	GTEx
rs11542549	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191063000-191076600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:191068600-191076600	Weak transcription	Fetal Kidney	kidney
3	chr3:191068800-191078800	Weak transcription	Fetal Brain Male	brain
4	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:191071000-191076000	Weak transcription	Primary T cells from cord blood	blood
6	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:191071200-191076800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:191071200-191078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191071200-191078800	Weak transcription	Lung	lung
10	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
11	chr3:191071400-191078400	Weak transcription	Fetal Intestine Small	intestine
12	chr3:191071400-191078800	Weak transcription	Gastric	stomach
13	chr3:191071400-191078800	Weak transcription	Pancreas	Pancrea
14	chr3:191071400-191078800	Weak transcription	Spleen	Spleen
15	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
16	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:191072400-191076400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:191072800-191076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:191073200-191077600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:191073200-191078000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:191073400-191077600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:191073400-191077800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:191073400-191079200	Weak transcription	Fetal Thymus	thymus
26	chr3:191073600-191077400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr3:191073600-191077600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:191073600-191083000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:191073800-191077400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:191073800-191079000	Weak transcription	Brain Angular Gyrus	brain
32	chr3:191074000-191077200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr3:191074200-191077600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:191074200-191078800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:191074400-191078600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:191074400-191079200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:191074600-191080400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
39	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:191074800-191076000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:191074800-191076000	Enhancers	Right Ventricle	heart
42	chr3:191074800-191078400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:191074800-191078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:191074800-191078800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:191074800-191079200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:191074800-191080000	Strong transcription	HepG2	liver
47	chr3:191074800-191081800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:191074800-191083000	Strong transcription	Primary B cells from cord blood	blood
49	chr3:191074800-191085800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:191074800-191094200	Weak transcription	A549	lung

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