Variant report

Variant	rs299205
Chromosome Location	chr5:118323121-118323122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39581660..39583614-chr5:118323067..118325473,2	MCF-7	breast:
2	chr5:118322493..118325395-chr5:118402550..118406560,4	K562	blood:
3	chr5:118322938..118326606-chr5:118602920..118605792,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction
ENSG00000249494	Chromatin interaction
ENSG00000239011	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11241493	1.00[JPT][hapmap]
rs13170553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs169917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213434	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213435	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431601	1.00[ASN][1000 genomes]
rs2431602	1.00[ASN][1000 genomes]
rs2442123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs299191	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs299194	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs299201	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299202	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299206	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299208	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs299209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs299214	1.00[JPT][hapmap]
rs368569	0.81[EUR][1000 genomes]
rs411110	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333791	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv969271	chr5:118317943-118323256	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs299205	FAM170A	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118314600-118323400	Weak transcription	Aorta	Aorta
2	chr5:118316000-118323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:118316200-118323200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:118316200-118323400	Weak transcription	Ovary	ovary
5	chr5:118316200-118323800	Weak transcription	Gastric	stomach
6	chr5:118319200-118323200	Weak transcription	Fetal Thymus	thymus
7	chr5:118320000-118323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:118321000-118323200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:118321000-118323200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:118321000-118323200	Weak transcription	Osteobl	bone
11	chr5:118321000-118323400	Weak transcription	HSMMtube	muscle
12	chr5:118321000-118323400	Weak transcription	NHLF	lung
13	chr5:118321200-118323200	Weak transcription	NHDF-Ad	bronchial
14	chr5:118321800-118323200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr5:118322200-118323400	Enhancers	Primary B cells from cord blood	blood
16	chr5:118322200-118323400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:118322400-118323200	Enhancers	Fetal Intestine Large	intestine
18	chr5:118322400-118323200	Enhancers	HepG2	liver
19	chr5:118322400-118323400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:118322400-118323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:118322400-118324800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:118322600-118323200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:118322800-118323200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:118322800-118323200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr5:118322800-118323200	Enhancers	NHEK	skin
26	chr5:118322800-118323400	Enhancers	Primary B cells from peripheral blood	blood
27	chr5:118322800-118323400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:118322800-118323400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr5:118322800-118323600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr5:118322800-118323600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr5:118322800-118324400	Active TSS	Fetal Muscle Leg	muscle
32	chr5:118323000-118323200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr5:118323000-118323200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:118323000-118323200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:118323000-118323200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:118323000-118323200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:118323000-118323200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:118323000-118323200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:118323000-118323200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:118323000-118323200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr5:118323000-118323200	Enhancers	Fetal Heart	heart
42	chr5:118323000-118323200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr5:118323000-118323200	Active TSS	Rectal Smooth Muscle	rectum
44	chr5:118323000-118323200	Enhancers	Stomach Mucosa	stomach
45	chr5:118323000-118323200	Enhancers	Stomach Smooth Muscle	stomach
46	chr5:118323000-118323400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr5:118323000-118323400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr5:118323000-118323400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr5:118323000-118323400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:118323000-118323400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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