Variant report

Variant	rs4677725
Chromosome Location	chr3:191087147-191087148
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	chr3:191084566..191087269-chr3:191092450..191094970,3	MCF-7	breast:
2	chr3:191071589..191073614-chr3:191084774..191087547,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11542549	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1435062	0.98[ASN][1000 genomes]
rs1473869	0.87[ASN][1000 genomes]
rs1520202	0.84[ASN][1000 genomes]
rs1520203	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1609926	0.95[ASN][1000 genomes]
rs16822378	0.95[ASN][1000 genomes]
rs16822382	0.95[ASN][1000 genomes]
rs16866487	0.87[ASN][1000 genomes]
rs16866504	1.00[ASN][1000 genomes]
rs16866505	1.00[ASN][1000 genomes]
rs17753967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17810246	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17810282	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17838893	0.87[ASN][1000 genomes]
rs2056333	0.87[ASN][1000 genomes]
rs2364379	0.91[ASN][1000 genomes]
rs28715898	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796219	0.84[ASN][1000 genomes]
rs3959143	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677631	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677632	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677726	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677727	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174842	0.87[ASN][1000 genomes]
rs57211729	0.99[ASN][1000 genomes]
rs58141749	0.96[ASN][1000 genomes]
rs58645265	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59709586	0.92[ASN][1000 genomes]
rs61250936	0.90[ASN][1000 genomes]
rs6444541	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73185209	0.90[ASN][1000 genomes]
rs73185210	0.92[ASN][1000 genomes]
rs73185213	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73185226	1.00[ASN][1000 genomes]
rs73185228	0.98[ASN][1000 genomes]
rs73185240	0.96[ASN][1000 genomes]
rs73185255	0.96[ASN][1000 genomes]
rs73185263	0.95[ASN][1000 genomes]
rs73185284	0.91[ASN][1000 genomes]
rs73185287	0.91[ASN][1000 genomes]
rs73185288	0.89[ASN][1000 genomes]
rs73201627	0.84[ASN][1000 genomes]
rs73201628	0.84[ASN][1000 genomes]
rs73201630	0.84[ASN][1000 genomes]
rs73201631	0.84[ASN][1000 genomes]
rs7637196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642387	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648886	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290986	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823680	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824437	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839751	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843934	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863255	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876944	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4677725	CCDC50	cis	Artery Tibial	GTEx
rs4677725	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:112 , 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	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
4	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
5	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
10	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:191074800-191094200	Weak transcription	A549	lung
12	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
13	chr3:191076000-191088800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:191076000-191092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:191076200-191091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:191077600-191094200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:191078000-191087600	Weak transcription	Psoas Muscle	Psoas
18	chr3:191078000-191089200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:191079400-191093000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:191079400-191094200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:191079400-191094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:191079600-191087600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:191079600-191088800	Weak transcription	Fetal Brain Male	brain
25	chr3:191079600-191089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:191079600-191089800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:191079600-191092600	Weak transcription	Primary T cells from cord blood	blood
28	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
29	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:191079600-191121200	Weak transcription	Gastric	stomach
31	chr3:191079800-191094200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:191080000-191087600	Weak transcription	Fetal Kidney	kidney
33	chr3:191080200-191094600	Weak transcription	Stomach Mucosa	stomach
34	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
36	chr3:191080400-191092800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:191080600-191087600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:191080600-191088800	Weak transcription	Lung	lung
39	chr3:191080600-191092800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:191080600-191094200	Weak transcription	Right Ventricle	heart
41	chr3:191080600-191094400	Weak transcription	Brain Angular Gyrus	brain
42	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:191080800-191087400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:191081200-191088000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:191081600-191087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:191081600-191087400	Weak transcription	Fetal Thymus	thymus
47	chr3:191081600-191094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:191081800-191087400	Weak transcription	HSMMtube	muscle
49	chr3:191081800-191088600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:191081800-191090200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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