Variant report

Variant	rs4687993
Chromosome Location	chr3:119010130-119010131
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	chr3:119009764..119012007-chr3:119036606..119039583,2	MCF-7	breast:
2	chr3:119008281..119010975-chr3:119011363..119014230,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000031081	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10934489	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710080	0.84[AFR][1000 genomes]
rs11914541	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916079	0.91[ASN][1000 genomes]
rs11918598	0.80[MEX][hapmap]
rs1542233	0.83[ASW][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2717260	0.88[CEU][hapmap]
rs2717266	0.83[EUR][1000 genomes]
rs56269733	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6438517	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6775982	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6800377	0.91[ASN][1000 genomes]
rs6800491	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620780	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622994	0.94[ASW][hapmap];0.94[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623525	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625392	0.94[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7640033	0.88[CEU][hapmap]
rs7649480	0.82[AFR][1000 genomes]
rs7649558	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9827972	0.85[TSI][hapmap]
rs9834125	0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4687993	IQCB1	cis	cerebellum	SCAN
rs4687993	CD86	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119007800-119012400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119008400-119010400	Enhancers	Right Ventricle	heart
3	chr3:119008600-119011000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:119008600-119011000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:119008600-119011800	Weak transcription	Placenta	Placenta
6	chr3:119008800-119011000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:119008800-119011000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:119008800-119011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:119008800-119011200	Weak transcription	GM12878-XiMat	blood
10	chr3:119008800-119011400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:119008800-119011400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:119008800-119011600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:119008800-119012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:119008800-119012600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:119008800-119012600	Weak transcription	Esophagus	oesophagus
16	chr3:119008800-119012800	Weak transcription	Spleen	Spleen
17	chr3:119009000-119011000	Weak transcription	Primary T cells from cord blood	blood
18	chr3:119009000-119011000	Weak transcription	Fetal Thymus	thymus
19	chr3:119009000-119011400	Weak transcription	Lung	lung
20	chr3:119009000-119011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:119009000-119012000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:119009200-119010600	Enhancers	Fetal Heart	heart
23	chr3:119009200-119011400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:119009200-119011400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:119009400-119010400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:119009400-119011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:119009400-119011600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:119009800-119010400	Enhancers	Fetal Intestine Large	intestine
29	chr3:119009800-119011000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:119009800-119011200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:119010000-119010200	Enhancers	Pancreatic Islets	Pancreatic Islet

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