Variant report

Variant	rs4479529
Chromosome Location	chr22:29934837-29934838
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	chr22:29932048..29935657-chr22:29948099..29949813,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1058642	0.87[EUR][1000 genomes]
rs11090569	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12161054	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2072301	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240638	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267147	0.85[EUR][1000 genomes]
rs2270077	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2348672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348677	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35404981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4470427	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6006178	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67292640	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7292442	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737975	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737980	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8142111	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs867088	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9608781	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9613940	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613942	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613943	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613956	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9613957	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9613958	0.83[EUR][1000 genomes]
rs9613961	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9613963	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9613965	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs999458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4479529	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs4479529	THOC5	cis	Artery Tibial	GTEx
rs4479529	THOC5	cis	Thyroid	GTEx
rs4479529	THOC5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr22:29902200-29937000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr22:29902400-29941200	Strong transcription	Placenta	Placenta
10	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:29910800-29937000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr22:29911200-29938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
18	chr22:29917800-29942400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29919000-29946600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:29919200-29941000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr22:29919200-29946600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr22:29919200-29946800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:29919400-29941000	Strong transcription	NH-A	brain
25	chr22:29919400-29941200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr22:29919400-29941600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr22:29919400-29941600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:29919400-29941800	Strong transcription	Primary T cells from cord blood	blood
29	chr22:29919400-29942000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:29919400-29942000	Strong transcription	Fetal Brain Female	brain
31	chr22:29919400-29942200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr22:29919400-29942200	Strong transcription	Dnd41	blood
33	chr22:29919400-29942400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr22:29919400-29942400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr22:29919400-29942400	Strong transcription	Osteobl	bone
36	chr22:29919400-29945200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr22:29919400-29946200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr22:29919400-29946600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:29919400-29946800	Strong transcription	Fetal Muscle Leg	muscle
40	chr22:29919400-29947000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:29919400-29947000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:29919600-29942200	Strong transcription	Brain Hippocampus Middle	brain
43	chr22:29919600-29945400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr22:29919600-29945400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:29919800-29937000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:29919800-29939200	Strong transcription	Brain Anterior Caudate	brain
47	chr22:29919800-29941200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr22:29919800-29945800	Strong transcription	Thymus	Thymus
49	chr22:29921000-29945400	Strong transcription	Liver	Liver
50	chr22:29921200-29942000	Strong transcription	Fetal Intestine Large	intestine

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