Variant report

Variant	rs7207225
Chromosome Location	chr17:45985414-45985415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45985387..45988064-chr17:45989640..45992704,3	MCF-7	breast:
2	chr17:45985355..45989671-chr17:46017595..46019779,4	MCF-7	breast:
3	chr17:45982730..45985492-chr17:46018085..46020258,2	MCF-7	breast:
4	chr17:45922908..45925647-chr17:45983799..45986055,2	MCF-7	breast:
5	chr17:45985212..45987744-chr17:46022606..46024465,2	MCF-7	breast:
6	chr17:45985099..45987381-chr17:45994807..45997367,2	MCF-7	breast:
7	chr17:45981397..45984686-chr17:45985250..45989369,5	K562	blood:

Variant related genes	Relation type
ENSG00000108439	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000234494	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11079800	0.85[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap]
rs11079802	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11650395	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11651753	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11653445	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939572	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16949418	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16949720	0.95[JPT][hapmap]
rs2002136	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs2325748	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525095	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2525109	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2525110	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2597169	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2875735	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs3764394	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764398	0.85[ASN][1000 genomes]
rs4794331	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs59811700	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71377324	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220104	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs72833491	0.99[ASN][1000 genomes]
rs72840233	0.98[ASN][1000 genomes]
rs8079333	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899097	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7207225	RPRML	cis	parietal	SCAN
rs7207225	DBF4B	cis	parietal	SCAN
rs7207225	SP2	cis	lymphoblastoid	seeQTL
rs7207225	CALCOCO2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
4	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
5	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
7	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:45976800-45987000	Strong transcription	Fetal Intestine Small	intestine
10	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:45977800-45992000	Weak transcription	Dnd41	blood
13	chr17:45977800-45992600	Weak transcription	Fetal Intestine Large	intestine
14	chr17:45977800-45992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
16	chr17:45979200-45987400	Weak transcription	Thymus	Thymus
17	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:45980000-45992600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
21	chr17:45980200-45986000	Enhancers	Fetal Muscle Trunk	muscle
22	chr17:45980200-46001800	Weak transcription	K562	blood
23	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr17:45980400-45992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr17:45980800-45987000	Enhancers	Left Ventricle	heart
28	chr17:45980800-45992600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:45981600-45985600	Enhancers	Lung	lung
30	chr17:45981600-45986000	Enhancers	Fetal Heart	heart
31	chr17:45981800-45987200	Enhancers	Adipose Nuclei	Adipose
32	chr17:45982200-45988400	Strong transcription	Primary T cells from cord blood	blood
33	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
34	chr17:45982600-45985800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr17:45982600-45992600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:45982600-45992600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:45982600-45992800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr17:45982800-45985800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr17:45982800-45993000	Weak transcription	NHEK	skin
41	chr17:45983000-45988200	Weak transcription	Liver	Liver
42	chr17:45983000-45993800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:45983200-45985800	Enhancers	Brain Anterior Caudate	brain
46	chr17:45983200-45988000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr17:45983200-45992400	Weak transcription	Colonic Mucosa	Colon
48	chr17:45983200-45992600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:45983200-45992600	Weak transcription	Gastric	stomach
50	chr17:45983200-45993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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