Variant report

Variant	rs11914618
Chromosome Location	chr3:78724494-78724495
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	CTCF	chr3:78724360-78724510	BE2_C	brain:	n/a	n/a
2	CTCF	chr3:78724350-78724589	MCF-7	breast:	n/a	n/a
3	MYC	chr3:78724478-78724614	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:78724360-78724510	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:78724380-78724530	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:78724471-78724780	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:78724367-78724591	MCF-7	breast:	n/a	n/a
8	CTCF	chr3:78724355-78724600	MCF-7	breast:	n/a	n/a
9	CEBPB	chr3:78724298-78724566	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:78724370-78724569	MCF-7	breast:	n/a	n/a
11	CTCF	chr3:78724332-78724577	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:78724475-78724779	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78718158..78720294-chr3:78723664..78725642,2	MCF-7	breast:

Variant related genes	Relation type
ROBO1	TF binding region
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10049014	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10049102	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10428105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11920344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11925970	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11928868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1395784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1457659	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs17016466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17375110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17375496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17375739	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1865860	0.84[CEU][hapmap]
rs1865861	0.89[CEU][hapmap]
rs1865863	0.90[CEU][hapmap]
rs2271151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3732663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3773220	0.85[CEU][hapmap]
rs3773226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3773231	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3773234	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap]
rs3773240	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs3821601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821602	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3821603	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4263256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6769933	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6787349	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6788434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6788511	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7610686	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7613490	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7616495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7622194	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7624482	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7653782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs767182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9808950	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9819398	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9823359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9866912	0.89[CEU][hapmap]
rs9880072	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9880316	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9882811	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs997274	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]

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	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
2	chr3:78667200-78751200	Weak transcription	Esophagus	oesophagus
3	chr3:78676800-78730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:78679200-78733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:78679400-78730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:78679400-78736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:78693400-78730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:78694200-78730600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:78694400-78733200	Weak transcription	Fetal Kidney	kidney
10	chr3:78702800-78730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:78703200-78739200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:78706400-78736200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:78706600-78735200	Weak transcription	Primary T cells from cord blood	blood
14	chr3:78706600-78736400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:78707000-78735400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:78711800-78726800	Weak transcription	Fetal Stomach	stomach
17	chr3:78716000-78724800	Weak transcription	HSMM	muscle
18	chr3:78716000-78739600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:78716600-78733000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:78717600-78733200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:78717600-78739600	Weak transcription	Osteobl	bone
22	chr3:78717800-78736800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:78717800-78745200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:78717800-78748400	Weak transcription	Ovary	ovary
25	chr3:78718600-78739200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:78719400-78730400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:78719400-78736800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:78719600-78730600	Weak transcription	HepG2	liver
29	chr3:78719600-78753000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:78720000-78730400	Weak transcription	Fetal Lung	lung
31	chr3:78720000-78737800	Weak transcription	Fetal Brain Female	brain
32	chr3:78720000-78753200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:78720200-78731600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:78721400-78725000	Weak transcription	Fetal Brain Male	brain
35	chr3:78721400-78730400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:78721400-78730600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:78724000-78724800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:78724400-78724800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr3:78724400-78730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:78724400-78738200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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