Variant report

Variant	rs176820
Chromosome Location	chr3:191094659-191094660
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:191059055..191059627-chr3:191094564..191095535,2	MCF-7	breast:
2	chr3:191059991..191062232-chr3:191093910..191095757,2	MCF-7	breast:
3	chr3:191084566..191087269-chr3:191092450..191094970,3	MCF-7	breast:
4	chr3:191093711..191095973-chr3:191100119..191102866,3	K562	blood:
5	chr3:191077443..191079783-chr3:191093772..191095748,2	K562	blood:
6	chr3:191094269..191095897-chr3:191095965..191098815,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152492	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10937477	0.82[CHB][hapmap]
rs1465737	0.84[EUR][1000 genomes]
rs1473866	0.82[CHB][hapmap]
rs150506	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs159489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs186063	1.00[CHB][hapmap]
rs186066	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs188384	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs192671	0.82[CHB][hapmap]
rs293797	0.82[CHB][hapmap]
rs293798	0.82[CHB][hapmap]
rs293800	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs293802	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs293804	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs293805	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs293806	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs293808	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs293844	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs293846	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs293851	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs297396	0.82[CHB][hapmap]
rs367747	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs368665	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs369174	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs373035	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs381090	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs383075	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs390744	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs401465	0.82[CHB][hapmap]
rs426466	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs432085	0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs434556	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs437244	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs448133	0.82[CHB][hapmap]
rs4677734	0.82[CHB][hapmap]
rs4677735	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs523270	0.82[CHB][hapmap]
rs525774	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs526785	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs529523	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566548	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6779820	0.82[CHB][hapmap]
rs6953	0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs697905	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs709142	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	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
8	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
rs176820	CCDC50	cis	Thyroid	GTEx
rs176820	CCDC50	cis	Artery Tibial	GTEx
rs176820	CCDC50	cis	Artery Aorta	GTEx

Chromatin state (count:109 , 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	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
7	chr3:191079400-191094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
10	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:191079600-191121200	Weak transcription	Gastric	stomach
12	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
14	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:191083000-191094800	Strong transcription	Liver	Liver
16	chr3:191085000-191096000	Weak transcription	K562	blood
17	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:191087800-191100000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:191089000-191097200	Weak transcription	Fetal Thymus	thymus
23	chr3:191090800-191096000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:191093200-191095000	Strong transcription	Primary B cells from cord blood	blood
25	chr3:191093200-191095400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:191093200-191095600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:191093400-191096400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:191093400-191097400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:191093400-191097400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:191093400-191097400	Weak transcription	HepG2	liver
31	chr3:191093400-191097600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:191093400-191098200	Weak transcription	Left Ventricle	heart
33	chr3:191093400-191099200	Weak transcription	Aorta	Aorta
34	chr3:191093400-191099200	Weak transcription	Lung	lung
35	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
37	chr3:191093600-191098000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:191093600-191098400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:191093800-191094800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:191093800-191094800	Genic enhancers	Fetal Heart	heart
41	chr3:191093800-191095000	Enhancers	NHEK	skin
42	chr3:191093800-191097600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:191093800-191097800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:191093800-191098200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:191094000-191095400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:191094000-191096800	Enhancers	Osteobl	bone
47	chr3:191094000-191097000	Weak transcription	Placenta	Placenta
48	chr3:191094000-191098800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:191094200-191094800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:191094200-191094800	Enhancers	Cortex derived primary cultured neurospheres	brain

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