Variant report

Variant	rs12522073
Chromosome Location	chr5:178487452-178487453
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	chr5:178286798..178288918-chr5:178487242..178488938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10058386	0.92[EUR][1000 genomes]
rs10066034	1.00[JPT][hapmap]
rs10070609	0.81[AMR][1000 genomes]
rs10464079	0.82[AMR][1000 genomes]
rs11249612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1136377	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12515865	1.00[JPT][hapmap]
rs12517889	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12522721	1.00[JPT][hapmap]
rs1445844	0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs1445845	0.85[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs1445846	0.85[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs1549602	0.81[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs1549603	1.00[JPT][hapmap]
rs1826864	0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1972715	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2059776	0.85[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs2303644	1.00[JPT][hapmap]
rs3822592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3932173	0.82[JPT][hapmap]
rs4105175	0.82[JPT][hapmap]
rs4701026	0.80[TSI][hapmap]
rs4701031	0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs4701034	0.83[CEU][hapmap]
rs6601006	0.82[JPT][hapmap]
rs6601011	0.82[AMR][1000 genomes]
rs6601012	0.82[AMR][1000 genomes]
rs6601013	0.82[AMR][1000 genomes]
rs6601014	0.85[CEU][hapmap]
rs6864279	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6864287	0.83[AMR][1000 genomes]
rs6873398	0.82[JPT][hapmap]
rs6879226	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6879356	0.83[AMR][1000 genomes]
rs7717952	0.81[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs7736323	1.00[JPT][hapmap]
rs888762	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs890699	0.81[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs931618	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs931619	0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12522073	GRM6	cis	cerebellum	SCAN
rs12522073	PFN3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178486400-178488200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr5:178486600-178487800	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr5:178486600-178487800	Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr5:178486600-178487800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:178486600-178487800	Active TSS	Brain Hippocampus Middle	brain
6	chr5:178486600-178487800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:178486600-178487800	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:178486600-178487800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr5:178486600-178487800	Active TSS	Fetal Heart	heart
10	chr5:178486600-178487800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr5:178486600-178487800	Active TSS	Right Atrium	heart
12	chr5:178486600-178488000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
13	chr5:178486600-178488000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:178486600-178488000	Active TSS	Brain Angular Gyrus	brain
15	chr5:178486600-178488000	Active TSS	Colon Smooth Muscle	Colon
16	chr5:178486600-178488000	Active TSS	Psoas Muscle	Psoas
17	chr5:178486600-178488200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:178486600-178488200	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr5:178486600-178488200	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr5:178486600-178488600	Active TSS	Fetal Kidney	kidney
21	chr5:178486600-178489000	Active TSS	Rectal Smooth Muscle	rectum
22	chr5:178486800-178487600	Active TSS	Primary monocytes fromperipheralblood	blood
23	chr5:178486800-178487600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:178486800-178487800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:178486800-178487800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr5:178486800-178487800	Active TSS	Primary T cells from cord blood	blood
27	chr5:178486800-178487800	Active TSS	Primary T cells fromperipheralblood	blood
28	chr5:178486800-178487800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:178486800-178487800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:178486800-178487800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr5:178486800-178487800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:178486800-178487800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:178486800-178487800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr5:178486800-178487800	Active TSS	Fetal Muscle Leg	muscle
35	chr5:178486800-178487800	Active TSS	Stomach Mucosa	stomach
36	chr5:178486800-178487800	Active TSS	HMEC	breast
37	chr5:178486800-178487800	Active TSS	NHEK	skin
38	chr5:178486800-178488000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr5:178486800-178488000	Active TSS	Aorta	Aorta
40	chr5:178486800-178488000	Active TSS	Brain Cingulate Gyrus	brain
41	chr5:178486800-178488000	Active TSS	Brain Substantia Nigra	brain
42	chr5:178486800-178488000	Active TSS	Colonic Mucosa	Colon
43	chr5:178486800-178488000	Active TSS	Fetal Brain Male	brain
44	chr5:178486800-178488000	Active TSS	Ovary	ovary
45	chr5:178486800-178488000	Active TSS	Right Ventricle	heart
46	chr5:178486800-178488000	Active TSS	Osteobl	bone
47	chr5:178486800-178488200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:178486800-178488200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:178486800-178488200	Active TSS	Brain Anterior Caudate	brain
50	chr5:178486800-178488200	Active TSS	NH-A	brain

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