Variant report

Variant	rs8028002
Chromosome Location	chr15:76024857-76024858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76021238..76025261-chr15:76028458..76030884,3	MCF-7	breast:
2	chr15:76019014..76021554-chr15:76023270..76025414,2	MCF-7	breast:
3	chr15:76024847..76025757-chr15:76094197..76095031,3	MCF-7	breast:
4	chr15:76024107..76026384-chr15:76031039..76032917,2	MCF-7	breast:
5	chr15:76023899..76025633-chr15:76028640..76031037,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256530	Chromatin interaction
ENSG00000246877	Chromatin interaction
ENSG00000260288	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10163112	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10519109	0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634290	0.92[JPT][hapmap]
rs11636280	0.82[JPT][hapmap]
rs11852712	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854305	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858818	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898509	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899163	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899303	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900007	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12900167	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903661	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904654	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12905062	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905730	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13329104	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1823175	0.87[ASN][1000 genomes]
rs1850261	0.87[ASN][1000 genomes]
rs1964473	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs1964474	0.84[ASN][1000 genomes]
rs1996302	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996303	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002668	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2004630	0.84[ASN][1000 genomes]
rs2004920	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2009508	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010392	0.88[ASN][1000 genomes]
rs2017312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290484	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2405718	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2405882	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28404806	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28541422	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28615348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28651447	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28657001	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28688252	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28695212	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28695716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744558	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28833005	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28837134	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34243492	0.85[ASN][1000 genomes]
rs34402412	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34469290	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34571038	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34605750	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34611707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34941412	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35019194	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35135316	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35136767	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35147271	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35411779	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35575236	0.83[AMR][1000 genomes]
rs35745834	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35842909	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36057011	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751536	1.00[JPT][hapmap]
rs3845233	0.86[ASN][1000 genomes]
rs3845234	0.86[ASN][1000 genomes]
rs3850092	0.87[ASN][1000 genomes]
rs3861184	0.86[ASN][1000 genomes]
rs4503758	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616261	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs55744943	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57905971	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60214227	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66838310	0.85[ASN][1000 genomes]
rs67908345	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71403504	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71403505	0.82[AMR][1000 genomes]
rs71462532	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7163633	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165531	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181595	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74026532	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026234	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037672	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8041390	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8041670	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
4	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8028002	ARID3B	cis	cerebellum	SCAN
rs8028002	FBXO22	cis	parietal	SCAN
rs8028002	UBE2Q2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76013600-76025000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:76013800-76029800	Weak transcription	HSMM	muscle
3	chr15:76016800-76025200	Weak transcription	Pancreas	Pancrea
4	chr15:76020000-76025000	Weak transcription	Esophagus	oesophagus
5	chr15:76020200-76025200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:76020600-76030200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:76020800-76026400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:76021000-76030200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:76021000-76030200	Weak transcription	HMEC	breast
10	chr15:76021400-76029600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:76022000-76028800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:76023000-76026000	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:76023400-76025600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:76023600-76025000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr15:76023600-76025200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:76023600-76025400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:76023600-76025400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:76023600-76025400	Flanking Active TSS	Fetal Lung	lung
19	chr15:76023600-76025600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr15:76023600-76025600	Enhancers	Fetal Thymus	thymus
21	chr15:76023600-76025800	Enhancers	Fetal Muscle Leg	muscle
22	chr15:76023800-76025000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:76023800-76025000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr15:76023800-76025000	Enhancers	Stomach Smooth Muscle	stomach
25	chr15:76023800-76025200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:76023800-76025200	Enhancers	Fetal Heart	heart
27	chr15:76023800-76025200	Enhancers	NHLF	lung
28	chr15:76023800-76025400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:76023800-76025600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr15:76023800-76025600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr15:76023800-76025600	Enhancers	Duodenum Mucosa	Duodenum
32	chr15:76023800-76025600	Enhancers	Ovary	ovary
33	chr15:76023800-76025600	Enhancers	Right Ventricle	heart
34	chr15:76023800-76027000	Enhancers	Placenta	Placenta
35	chr15:76024000-76025000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:76024000-76025000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:76024000-76025000	Enhancers	NHDF-Ad	bronchial
38	chr15:76024000-76025200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr15:76024000-76025200	Enhancers	Fetal Intestine Large	intestine
40	chr15:76024000-76025200	Enhancers	Right Atrium	heart
41	chr15:76024000-76025200	Enhancers	HUVEC	blood vessel
42	chr15:76024000-76025400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:76024000-76025400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:76024000-76025600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr15:76024000-76025600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:76024000-76025600	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:76024000-76027200	Enhancers	Fetal Kidney	kidney
48	chr15:76024200-76025000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr15:76024200-76025200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:76024200-76025200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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