Variant report

Variant	rs28706464
Chromosome Location	chr9:98235310-98235311
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	chr9:98233432..98236653-chr9:98236835..98241063,4	MCF-7	breast:
2	chr9:98233664..98236470-chr9:98268989..98270628,2	K562	blood:

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10512249	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16909892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16909898	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16909902	0.91[CEU][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16909904	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16909922	0.84[EUR][1000 genomes]
rs1805155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036963	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282040	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282041	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282043	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs28372566	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28418339	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28427480	0.84[EUR][1000 genomes]
rs28446116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28446321	0.84[EUR][1000 genomes]
rs28448271	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28469297	1.00[MEX][hapmap]
rs28474857	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28493225	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28494679	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28510415	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28520225	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28535421	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28535536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28583690	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28673156	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28733891	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3780573	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3824488	0.83[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56149656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59015093	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59925771	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60150206	0.83[EUR][1000 genomes]
rs60417486	0.83[EUR][1000 genomes]
rs867452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	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
2	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
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28706464	FBP2	cis	parietal	SCAN
rs28706464	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
3	chr9:98225800-98239600	Weak transcription	HMEC	breast
4	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
7	chr9:98226000-98251000	Weak transcription	Osteobl	bone
8	chr9:98226200-98238400	Weak transcription	NH-A	brain
9	chr9:98226200-98239000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:98226200-98239400	Weak transcription	NHEK	skin
11	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
12	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:98226400-98239200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:98226400-98239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
18	chr9:98226600-98239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:98226600-98239200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:98226600-98239400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:98226800-98239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
29	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
31	chr9:98227200-98239200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:98227400-98239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:98227400-98242000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:98227400-98242800	Strong transcription	Adipose Nuclei	Adipose
38	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
39	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:98228000-98240400	Strong transcription	Left Ventricle	heart
41	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:98228200-98238600	Strong transcription	Brain Substantia Nigra	brain
43	chr9:98228600-98239200	Strong transcription	Brain Hippocampus Middle	brain
44	chr9:98229000-98238800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr9:98229400-98237400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:98229600-98238200	Strong transcription	Brain Germinal Matrix	brain
47	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:98231000-98239800	Weak transcription	HSMM	muscle
49	chr9:98231200-98237800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr9:98231400-98237400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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