Variant report

Variant	rs11704899
Chromosome Location	chr22:29918482-29918483
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	chr22:29910824..29913360-chr22:29916789..29919438,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006396	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs10427824	0.83[EUR][1000 genomes]
rs165625	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs165668	0.85[ASN][1000 genomes]
rs16987832	0.92[CEU][hapmap]
rs174650	1.00[CHB][hapmap]
rs174651	0.85[ASN][1000 genomes]
rs2074951	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2188120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2247753	0.94[CEU][hapmap]
rs2267152	0.83[CEU][hapmap]
rs2527336	0.80[CEU][hapmap];1.00[LWK][hapmap]
rs2530656	0.94[CEU][hapmap]
rs2530664	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs2531848	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs458196	0.94[CEU][hapmap]
rs465742	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55652051	0.87[ASN][1000 genomes]
rs5752933	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs5752937	0.91[ASN][1000 genomes]
rs5763269	1.00[CHB][hapmap]
rs5763286	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs5763287	0.89[ASN][1000 genomes]
rs5763292	0.91[ASN][1000 genomes]
rs5763293	0.87[ASN][1000 genomes]
rs5763305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs57995869	0.81[EUR][1000 genomes]
rs8135828	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs8140848	0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11704899	THOC5	cis	Artery Tibial	GTEx
rs11704899	THOC5	cis	lung	GTEx
rs11704899	THOC5	cis	Artery Aorta	GTEx
rs11704899	THOC5	cis	Muscle Skeletal	GTEx
rs11704899	THOC5	cis	Esophagus Muscularis	GTEx
rs11704899	THOC5	cis	Adipose Subcutaneous	GTEx
rs11704899	THOC5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29897600-29934600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:29900400-29929000	Strong transcription	Fetal Stomach	stomach
4	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29900800-29929000	Strong transcription	Fetal Intestine Small	intestine
6	chr22:29900800-29930600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:29901200-29925200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr22:29901200-29929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr22:29902200-29937000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:29902400-29923800	Strong transcription	Lung	lung
16	chr22:29902400-29930000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:29902400-29941200	Strong transcription	Placenta	Placenta
18	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr22:29903600-29931000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr22:29904600-29927600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:29910800-29937000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:29911000-29918600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr22:29911200-29921400	Strong transcription	Adipose Nuclei	Adipose
26	chr22:29911200-29938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:29911400-29918600	Strong transcription	HepG2	liver
29	chr22:29911400-29930400	Strong transcription	HSMM	muscle
30	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr22:29913600-29925800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
33	chr22:29914000-29929600	Weak transcription	Fetal Heart	heart
34	chr22:29914200-29919400	Weak transcription	Psoas Muscle	Psoas
35	chr22:29914800-29921400	Strong transcription	Hela-S3	cervix
36	chr22:29915000-29924800	Weak transcription	Stomach Mucosa	stomach
37	chr22:29915400-29920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:29915400-29920600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr22:29915600-29920000	Weak transcription	Small Intestine	intestine
40	chr22:29916400-29926200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr22:29917200-29919400	Weak transcription	NHEK	skin
42	chr22:29917200-29919400	Weak transcription	NHLF	lung
43	chr22:29917400-29919400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:29917400-29919400	Weak transcription	HMEC	breast
45	chr22:29917400-29919400	Weak transcription	NHDF-Ad	bronchial
46	chr22:29917400-29920000	Weak transcription	Right Ventricle	heart
47	chr22:29917400-29925000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:29917800-29919400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:29917800-29919400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr22:29917800-29919400	Weak transcription	Muscle Satellite Cultured Cells	--

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