Variant report

Variant	rs4687770
Chromosome Location	chr3:51755065-51755066
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	chr3:51741483..51743641-chr3:51752692..51755400,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164082	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11919197	0.92[CEU][hapmap]
rs12487957	0.80[CHD][hapmap]
rs13090011	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3821829	0.92[CEU][hapmap]
rs4067	0.92[CEU][hapmap]
rs4234644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4355273	0.92[CEU][hapmap]
rs4468965	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4687771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687775	0.80[EUR][1000 genomes]
rs6775666	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4687770	TEX264	cis	Nerve Tibial	GTEx
rs4687770	MST1	cis	cerebellum	SCAN
rs4687770	HEMK1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51740200-51755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:51741800-51756000	Weak transcription	Gastric	stomach
3	chr3:51750800-51755600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:51751400-51755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:51752200-51755400	Weak transcription	Fetal Brain Female	brain
6	chr3:51752200-51756400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:51752600-51755800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:51752800-51755800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:51753000-51756200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:51753000-51756400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:51753200-51756200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:51753200-51756200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:51753400-51755400	Weak transcription	Fetal Brain Male	brain
14	chr3:51753400-51755400	Weak transcription	Spleen	Spleen
15	chr3:51753600-51755200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:51753600-51755200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:51753600-51755200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:51753600-51755200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:51753600-51755200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:51753600-51755400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:51753600-51755600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:51754200-51755200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:51754400-51755400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:51754600-51756400	Enhancers	Esophagus	oesophagus
25	chr3:51754600-51756600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:51754800-51756400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:51755000-51756000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:51755000-51756400	Enhancers	Primary T cells from cord blood	blood

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