Variant report

Variant	rs737975
Chromosome Location	chr22:29908849-29908850
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29907835..29909461-chr22:29910820..29913528,2	MCF-7	breast:
2	chr22:29907526..29909424-chr22:29918736..29921432,2	MCF-7	breast:
3	chr22:29907918..29910292-chr22:29913329..29915343,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1058642	0.89[EUR][1000 genomes]
rs11090569	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12161054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13056992	0.89[EUR][1000 genomes]
rs1807506	0.81[EUR][1000 genomes]
rs2072301	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240638	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267147	0.87[EUR][1000 genomes]
rs2270077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348672	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348677	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2881994	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35404981	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3940296	0.96[CEU][hapmap]
rs4470427	0.84[EUR][1000 genomes]
rs4479529	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6006178	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67292640	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs715490	0.96[CEU][hapmap]
rs7292442	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737980	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737981	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8142111	0.89[EUR][1000 genomes]
rs867088	0.87[EUR][1000 genomes]
rs9608781	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9608790	0.96[CEU][hapmap]
rs9608794	0.96[CEU][hapmap]
rs9608799	0.96[CEU][hapmap]
rs9613940	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613942	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613943	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613956	0.88[EUR][1000 genomes]
rs9613957	0.88[EUR][1000 genomes]
rs9613958	0.85[EUR][1000 genomes]
rs9613961	0.84[EUR][1000 genomes]
rs9613963	0.82[EUR][1000 genomes]
rs9613965	0.82[EUR][1000 genomes]
rs9613970	0.96[CEU][hapmap]
rs9613971	0.96[CEU][hapmap]
rs9613975	0.96[CEU][hapmap]
rs9613984	0.96[CEU][hapmap]
rs9613999	0.96[CEU][hapmap]
rs9614004	0.91[CEU][hapmap]
rs9614005	0.96[CEU][hapmap]
rs9614006	0.96[CEU][hapmap]
rs9614011	0.95[CEU][hapmap]
rs9614018	0.96[CEU][hapmap]
rs999458	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs737975	THOC5	cis	Artery Tibial	GTEx
rs737975	THOC5	cis	Thyroid	GTEx
rs737975	THOC5	cis	Adipose Subcutaneous	GTEx
rs737975	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29894600-29914800	Weak transcription	Hela-S3	cervix
2	chr22:29895800-29916800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:29897600-29934600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29898400-29911400	Weak transcription	Fetal Kidney	kidney
6	chr22:29899800-29909600	Strong transcription	Primary T cells from cord blood	blood
7	chr22:29900400-29913200	Weak transcription	Fetal Heart	heart
8	chr22:29900400-29929000	Strong transcription	Fetal Stomach	stomach
9	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:29900600-29918000	Strong transcription	Fetal Thymus	thymus
11	chr22:29900800-29909000	Strong transcription	Fetal Brain Female	brain
12	chr22:29900800-29909600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr22:29900800-29909800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:29900800-29918000	Strong transcription	Fetal Muscle Leg	muscle
15	chr22:29900800-29929000	Strong transcription	Fetal Intestine Small	intestine
16	chr22:29900800-29930600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr22:29901000-29909000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr22:29901000-29909200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:29901000-29918000	Strong transcription	Fetal Intestine Large	intestine
20	chr22:29901000-29918400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:29901200-29909000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr22:29901200-29909000	Strong transcription	Liver	Liver
24	chr22:29901200-29909200	Strong transcription	Brain Hippocampus Middle	brain
25	chr22:29901200-29909800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr22:29901200-29909800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:29901200-29910200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr22:29901200-29913400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr22:29901200-29916600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr22:29901200-29917000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:29901200-29918000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr22:29901200-29925200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr22:29901200-29929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:29901400-29909000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr22:29901400-29909000	Strong transcription	Primary B cells from cord blood	blood
38	chr22:29901400-29909600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr22:29901400-29909800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr22:29901800-29918000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr22:29902000-29909600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr22:29902000-29909600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr22:29902000-29909600	Strong transcription	Osteobl	bone
46	chr22:29902000-29917800	Strong transcription	Brain Anterior Caudate	brain
47	chr22:29902000-29918000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr22:29902000-29918000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr22:29902200-29909000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr22:29902200-29909000	Strong transcription	Placenta Amnion	Placenta Amnion

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