Variant report

Variant	rs17062858
Chromosome Location	chr9:79272019-79272020
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	FOXM1	chr9:79271949-79272815	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr9:79271942-79272698	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr9:79271918-79272992	SK-N-SH	brain:	n/a	chr9:79272272-79272279
4	EP300	chr9:79271930-79272778	SK-N-SH	brain:	n/a	chr9:79272683-79272690
5	TEAD4	chr9:79271924-79272735	SK-N-SH	brain:	n/a	n/a
6	JUND	chr9:79271979-79272718	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr9:79271922-79272782	SK-N-SH	brain:	n/a	n/a
8	EP300	chr9:79271951-79272785	SK-N-SH	brain:	n/a	chr9:79272683-79272690
9	NFIC	chr9:79271982-79272845	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr9:79271966-79272749	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr9:79271988-79272730	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr9:79271783-79272941	SK-N-SH	brain:	n/a	chr9:79272272-79272279
13	TCF12	chr9:79271911-79272834	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79082022..79083727-chr9:79271380..79273433,2	MCF-7	breast:
2	chr9:79073700..79075810-chr9:79270098..79272693,3	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10521475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11144986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11144987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11144992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17062768	1.00[CEU][hapmap]
rs17062772	1.00[CEU][hapmap]
rs17062775	1.00[CEU][hapmap]
rs17062778	1.00[CEU][hapmap]
rs1854441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2067501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs499746	1.00[CEU][hapmap]
rs57389265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634063	0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs637207	1.00[CEU][hapmap]
rs644893	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7027074	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7028756	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7038619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7039310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7045505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7847922	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
3	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:79263600-79272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:79266000-79278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
9	chr9:79266600-79274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:79266600-79282200	Weak transcription	Brain Anterior Caudate	brain
11	chr9:79266800-79272600	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:79267000-79273200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:79267200-79273400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:79267600-79273400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:79268000-79272600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr9:79268200-79273400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:79268400-79272600	Enhancers	NHDF-Ad	bronchial
18	chr9:79268800-79273400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:79269000-79278000	Weak transcription	Aorta	Aorta
20	chr9:79269200-79273200	Weak transcription	Fetal Intestine Small	intestine
21	chr9:79269200-79273400	Weak transcription	Fetal Kidney	kidney
22	chr9:79269200-79275800	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:79269400-79274000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:79269400-79277000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:79269800-79272200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr9:79269800-79272800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr9:79269800-79282200	Weak transcription	Brain Substantia Nigra	brain
28	chr9:79270200-79272200	Weak transcription	Primary B cells from cord blood	blood
29	chr9:79270400-79272800	Enhancers	HUVEC	blood vessel
30	chr9:79270400-79273800	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:79270400-79277000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:79270400-79277200	Weak transcription	GM12878-XiMat	blood
33	chr9:79270400-79303000	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:79270600-79272800	Enhancers	NH-A	brain
35	chr9:79270600-79273400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr9:79270600-79273400	Weak transcription	Fetal Thymus	thymus
37	chr9:79270600-79273800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:79270600-79274000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:79270600-79274000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:79270600-79275000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:79270600-79278800	Weak transcription	Brain Angular Gyrus	brain
42	chr9:79271200-79273400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:79271200-79273600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr9:79271400-79273000	Enhancers	Small Intestine	intestine
45	chr9:79271400-79273800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:79271400-79274000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:79271600-79272200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:79271600-79272600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:79271600-79273600	Enhancers	Primary B cells from peripheral blood	blood
50	chr9:79271600-79285200	Weak transcription	Rectal Smooth Muscle	rectum

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