Variant report

Variant	rs12194966
Chromosome Location	chr6:24437611-24437612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:24437429-24437669	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
GPLD1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10946700	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946701	0.81[ASN][1000 genomes]
rs12192905	1.00[ASW][hapmap]
rs12198188	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199914	1.00[ASW][hapmap]
rs12211574	1.00[ASW][hapmap]
rs12524609	0.81[ASN][1000 genomes]
rs13191455	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs13192752	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13205577	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205780	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17247566	0.81[ASN][1000 genomes]
rs34089102	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35901848	0.88[ASN][1000 genomes]
rs3846833	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60830931	0.81[ASN][1000 genomes]
rs62400468	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6922313	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922631	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71544274	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762593	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7762901	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766620	0.81[ASN][1000 genomes]
rs9295624	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461010	1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461011	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461012	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461013	0.88[ASN][1000 genomes]
rs9461014	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9461015	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9467148	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467157	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467158	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467160	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467161	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467166	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467168	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9467170	0.88[ASN][1000 genomes]
rs9467171	0.81[ASN][1000 genomes]
rs9467172	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12194966	ZSCAN12	cis	cerebellum	SCAN
rs12194966	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24417400-24451800	Strong transcription	Liver	Liver
2	chr6:24421200-24448800	Weak transcription	Gastric	stomach
3	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
4	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:24424000-24456600	Weak transcription	Ovary	ovary
6	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
9	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:24427600-24439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:24427600-24439400	Weak transcription	Fetal Thymus	thymus
15	chr6:24427600-24440000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:24427600-24440000	Weak transcription	Dnd41	blood
17	chr6:24427600-24441800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:24427600-24445600	Weak transcription	Fetal Brain Female	brain
19	chr6:24427600-24456800	Weak transcription	Lung	lung
20	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
21	chr6:24428200-24438000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:24428200-24449400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:24428800-24445000	Weak transcription	Psoas Muscle	Psoas
24	chr6:24429000-24447800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
26	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:24429400-24438600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:24429400-24445000	Weak transcription	Brain Anterior Caudate	brain
29	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:24429600-24444800	Weak transcription	HepG2	liver
31	chr6:24429600-24455000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:24430800-24448400	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:24432600-24463800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:24433200-24441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:24433600-24451600	Weak transcription	Adipose Nuclei	Adipose
36	chr6:24435800-24438200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:24436200-24438400	Strong transcription	Primary T cells from cord blood	blood
38	chr6:24436200-24438600	Strong transcription	Fetal Stomach	stomach
39	chr6:24436200-24438600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr6:24436600-24437800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr6:24436600-24438000	Strong transcription	Thymus	Thymus
42	chr6:24436600-24438400	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:24437000-24438200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:24437200-24438000	Strong transcription	Pancreas	Pancrea
45	chr6:24437200-24438400	Strong transcription	Right Ventricle	heart
46	chr6:24437200-24438800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr6:24437400-24437800	Strong transcription	Left Ventricle	heart
48	chr6:24437400-24438200	Strong transcription	Aorta	Aorta
49	chr6:24437400-24438400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:24437600-24455400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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