Variant report

Variant	rs7789393
Chromosome Location	chr7:150089268-150089269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150087569..150089555-chr7:150095693..150097782,2	MCF-7	breast:
2	chr7:150029857..150032114-chr7:150088055..150089634,2	K562	blood:
3	chr7:150074153..150076577-chr7:150088438..150090486,2	MCF-7	breast:
4	chr7:150087867..150089522-chr7:150096166..150097868,2	MCF-7	breast:
5	chr7:150083034..150085973-chr7:150088222..150090536,2	MCF-7	breast:
6	chr7:150081650..150085104-chr7:150086628..150089328,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196456	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1010614	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10156097	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10250758	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10952253	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12538411	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880316	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373693	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373694	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4269440	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4725339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55988243	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333034	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6464062	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957480	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6957590	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970818	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7780011	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7791304	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7791479	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799903	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs7810242	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
5	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
11	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv465211	chr7:150035526-150104410	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
14	nsv608991	chr7:150035526-150104410	Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
15	nsv608992	chr7:150045910-150115183	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
16	esv1819714	chr7:150055837-150154944	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
17	nsv889462	chr7:150060163-150108536	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7789393	SSPO	cis	parietal	SCAN
rs7789393	LRRC61	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150077200-150094000	Weak transcription	Aorta	Aorta
2	chr7:150077400-150100800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:150077800-150093200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:150077800-150096000	Weak transcription	Right Atrium	heart
5	chr7:150077800-150096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:150077800-150097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:150078000-150100600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:150078200-150095200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:150078200-150097200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:150078200-150097200	Weak transcription	HUVEC	blood vessel
11	chr7:150078600-150096600	Weak transcription	NHEK	skin
12	chr7:150079800-150093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:150079800-150095600	Weak transcription	HMEC	breast
14	chr7:150080000-150100200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr7:150080200-150093600	Weak transcription	Gastric	stomach
16	chr7:150080200-150100200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:150080600-150092800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:150080800-150096400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:150081000-150094800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:150081200-150093600	Weak transcription	Esophagus	oesophagus
21	chr7:150083000-150090200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr7:150083000-150093800	Weak transcription	Colonic Mucosa	Colon
23	chr7:150084000-150092600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:150084000-150092800	Weak transcription	Lung	lung
25	chr7:150085800-150094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:150086000-150096800	Weak transcription	Osteobl	bone
27	chr7:150086200-150090400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:150086200-150091200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:150086200-150093000	Weak transcription	NHLF	lung
30	chr7:150086200-150093200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:150086200-150096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:150086400-150092600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:150086400-150092600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr7:150086400-150095000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:150086400-150097200	Weak transcription	Stomach Mucosa	stomach
36	chr7:150086400-150100400	Weak transcription	Brain Angular Gyrus	brain
37	chr7:150086400-150100600	Weak transcription	Fetal Brain Male	brain
38	chr7:150086600-150090200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:150086600-150090400	Weak transcription	Fetal Intestine Large	intestine
40	chr7:150086600-150091400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:150086600-150092000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr7:150086600-150092000	Weak transcription	Ovary	ovary
43	chr7:150086600-150092600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:150086600-150092600	Weak transcription	Brain Anterior Caudate	brain
45	chr7:150086600-150093400	Weak transcription	Right Ventricle	heart
46	chr7:150086600-150093600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:150086600-150093800	Weak transcription	Left Ventricle	heart
48	chr7:150086600-150097000	Weak transcription	NH-A	brain
49	chr7:150086800-150092600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:150086800-150093200	Weak transcription	Adipose Nuclei	Adipose

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