Variant report

Variant	rs7399073
Chromosome Location	chr12:51614050-51614051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51611953..51614531-chr12:51619084..51621846,2	MCF-7	breast:
2	chr12:51610491..51614628-chr12:51614796..51620409,6	K562	blood:
3	chr12:51565491..51567919-chr12:51611128..51615638,5	K562	blood:
4	chr12:51611105..51614311-chr12:51630494..51636750,15	K562	blood:
5	chr12:51610404..51614741-chr12:51616630..51621489,9	K562	blood:
6	chr12:51609133..51616659-chr12:51628963..51635200,14	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAZAP2-3	chr12:51611479-51615172	NONHSAT028246

No data

Variant related genes	Relation type
ENSG00000183283	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000269339	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10747608	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10783424	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs6580810	0.88[EUR][1000 genomes]
rs6580811	0.87[EUR][1000 genomes]
rs7398442	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7399018	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs7953955	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	esv3437746	chr12:51611385-51615983	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7399073	SPATS2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51612800-51614200	Enhancers	Fetal Brain Male	brain
2	chr12:51612800-51616200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:51612800-51619800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:51612800-51621000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:51612800-51622200	Weak transcription	Lung	lung
6	chr12:51612800-51622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:51613000-51616000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:51613000-51616200	Weak transcription	Brain Anterior Caudate	brain
9	chr12:51613000-51616200	Weak transcription	Brain Germinal Matrix	brain
10	chr12:51613000-51616200	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:51613000-51616200	Weak transcription	Gastric	stomach
12	chr12:51613000-51616200	Weak transcription	Ovary	ovary
13	chr12:51613000-51619000	Weak transcription	Fetal Brain Female	brain
14	chr12:51613000-51619200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:51613000-51619200	Weak transcription	Brain Angular Gyrus	brain
16	chr12:51613000-51621200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:51613000-51621200	Weak transcription	Fetal Stomach	stomach
18	chr12:51613000-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:51613200-51618600	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:51613400-51614200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:51613400-51616200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:51613400-51616200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:51613400-51616200	Weak transcription	Brain Substantia Nigra	brain
24	chr12:51613400-51616200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:51613400-51616200	Weak transcription	HUVEC	blood vessel
26	chr12:51613400-51617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:51613400-51621600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:51613400-51622400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:51613400-51631600	Weak transcription	Thymus	Thymus
30	chr12:51613400-51631800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:51613400-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:51613400-51632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:51613600-51616200	Weak transcription	Liver	Liver
34	chr12:51613600-51620000	Weak transcription	Fetal Intestine Small	intestine
35	chr12:51613600-51631800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:51613600-51631800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:51613600-51631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:51613800-51616200	Weak transcription	A549	lung
39	chr12:51613800-51616200	Weak transcription	K562	blood
40	chr12:51613800-51616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:51613800-51618600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:51613800-51619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:51613800-51623600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:51614000-51614200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:51614000-51616200	Weak transcription	Fetal Lung	lung
46	chr12:51614000-51618000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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