Variant report

Variant	rs7388704
Chromosome Location	chr9:98171417-98171418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98171235..98175849-chr9:98186797..98190089,10	MCF-7	breast:
2	chr9:98170943..98174116-chr9:98263782..98265821,3	K562	blood:
3	chr9:98171208..98173629-chr9:98175498..98177832,2	MCF-7	breast:
4	chr9:98167871..98172268-chr9:98186784..98190412,5	MCF-7	breast:
5	chr9:98162269..98164911-chr9:98170422..98173133,2	K562	blood:
6	chr9:98170943..98172976-chr9:98263782..98265543,2	K562	blood:
7	chr9:98170885..98173194-chr9:98189275..98191495,2	K562	blood:
8	chr9:98167948..98170232-chr9:98170329..98172486,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-1	chr9:98170781-98173959	NONHSAT133367

No data

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction
ENSG00000213761	Chromatin interaction
ENSG00000271384	Chromatin interaction
ENSG00000237857	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10821464	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10993529	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10993534	0.90[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004780	0.94[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036514	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404693	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28471674	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28679639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35041950	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35402806	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35431736	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs357521	0.90[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs357522	0.90[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs357552	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59710018	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62558314	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479605	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7868504	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs905615	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs913711	0.87[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9695482	0.88[CEU][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1045479	chr9:98115290-98172995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1051731	chr9:98154815-98201115	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98144000-98172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:98150600-98173600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:98160400-98188400	Weak transcription	Pancreas	Pancrea
4	chr9:98161800-98172200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:98168600-98172200	Weak transcription	A549	lung
6	chr9:98168800-98171600	Weak transcription	Hela-S3	cervix
7	chr9:98169000-98172400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:98169600-98171800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:98169600-98172200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:98169600-98172400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:98169600-98173800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:98169600-98173800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:98169800-98172200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:98169800-98172200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:98169800-98172400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:98169800-98172400	Weak transcription	Fetal Lung	lung
17	chr9:98169800-98183600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:98169800-98183800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:98170000-98172200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:98170000-98172200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:98170000-98172200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:98170400-98172400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:98171200-98172000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr9:98171400-98171600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:98171400-98172000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:98171400-98173200	Enhancers	Primary monocytes fromperipheralblood	blood

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