Variant report

Variant	rs6777671
Chromosome Location	chr3:69249010-69249011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:69248478-69250687	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr3:69248682-69250278	Hela-S3	cervix:	n/a	chr3:69249246-69249261 chr3:69249849-69249864 chr3:69249728-69249745
3	POLR2A	chr3:69248412-69250355	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr3:69248946-69250100	MCF10A-Er-Src	breast:	n/a	chr3:69249094-69249102 chr3:69249823-69249831 chr3:69249821-69249832
5	POLR2A	chr3:69248677-69250458	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr3:69248887-69249080	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr3:69248897-69249087	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13059488	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs13059687	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs4624565	0.87[CEU][hapmap]
rs56815074	0.97[ASN][1000 genomes]
rs56993809	0.86[ASN][1000 genomes]
rs57343254	0.86[ASN][1000 genomes]
rs57396300	0.86[ASN][1000 genomes]
rs57600863	0.89[ASN][1000 genomes]
rs57671407	0.97[ASN][1000 genomes]
rs57765607	0.96[ASN][1000 genomes]
rs58068554	0.97[ASN][1000 genomes]
rs58110267	0.96[ASN][1000 genomes]
rs60770504	0.97[ASN][1000 genomes]
rs61312273	0.86[ASN][1000 genomes]
rs6764666	0.94[ASN][1000 genomes]
rs6789821	0.96[ASN][1000 genomes]
rs72928330	0.84[ASN][1000 genomes]
rs72930208	0.96[ASN][1000 genomes]
rs72930216	0.86[ASN][1000 genomes]
rs72930219	0.86[ASN][1000 genomes]
rs72930239	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635306	0.97[ASN][1000 genomes]
rs7647940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9833167	0.86[CEU][hapmap]
rs9847983	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs9860235	0.87[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs9875511	0.86[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	esv3398378	chr3:69240573-69271936	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6777671	S100Z	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69231400-69249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:69231800-69249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:69232000-69249400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:69232000-69275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:69232800-69249200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:69242400-69281600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:69242600-69249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:69242600-69268800	Weak transcription	Spleen	Spleen
9	chr3:69244000-69264800	Weak transcription	Fetal Brain Female	brain
10	chr3:69244200-69261800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:69244600-69249400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:69246200-69249600	Weak transcription	HSMMtube	muscle
13	chr3:69246200-69266800	Weak transcription	HSMM	muscle
14	chr3:69246400-69249600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:69246400-69249600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:69246600-69249600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:69246600-69249600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:69246600-69249600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:69247000-69249600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:69247000-69249600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:69247000-69249600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:69247000-69254000	Weak transcription	Fetal Brain Male	brain
23	chr3:69247200-69253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:69247600-69249600	Active TSS	Duodenum Mucosa	Duodenum
25	chr3:69247600-69249800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr3:69247600-69249800	Enhancers	Fetal Heart	heart
27	chr3:69247800-69249600	Weak transcription	Fetal Lung	lung
28	chr3:69247800-69249600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:69247800-69250000	Active TSS	Placenta	Placenta
30	chr3:69248000-69249400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:69248000-69249800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:69248000-69250000	Active TSS	Liver	Liver
33	chr3:69248000-69250200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:69248000-69250200	Active TSS	Hela-S3	cervix
35	chr3:69248200-69249400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:69248200-69249600	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:69248200-69249600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:69248200-69250000	Active TSS	Esophagus	oesophagus
39	chr3:69248200-69250200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:69248200-69257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:69248400-69249200	Active TSS	Primary T cells fromperipheralblood	blood
42	chr3:69248400-69249200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:69248400-69249200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:69248400-69249200	Flanking Active TSS	Dnd41	blood
45	chr3:69248400-69249400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:69248400-69249600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr3:69248400-69249600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:69248400-69249600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:69248400-69249600	Active TSS	Brain Substantia Nigra	brain
50	chr3:69248400-69249800	Active TSS	Primary B cells from cord blood	blood

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