Variant report

Variant	rs7954510
Chromosome Location	chr12:40452236-40452237
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	chr12:39935467..39937094-chr12:40451858..40454102,2	K562	blood:
2	12:40441273-40454218..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10747989	0.83[CHB][hapmap]
rs11174732	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11564162	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954510	SLC2A13	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
2	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
4	chr12:40444000-40453400	Weak transcription	Right Ventricle	heart
5	chr12:40449200-40452400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:40449200-40452400	Weak transcription	Brain Anterior Caudate	brain
7	chr12:40449200-40452600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:40449200-40457000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:40449400-40452400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:40449400-40452400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:40449400-40452600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:40449400-40452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:40449400-40452600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:40449600-40452600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:40450000-40452400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:40451200-40455000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:40451400-40452400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:40451400-40453400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr12:40452000-40458600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:40452200-40452600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:40452200-40452800	Enhancers	Brain Substantia Nigra	brain
22	chr12:40452200-40453000	Enhancers	Brain Hippocampus Middle	brain
23	chr12:40452200-40453200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:40452200-40453400	Enhancers	Hela-S3	cervix
25	chr12:40452200-40453800	Enhancers	Brain Germinal Matrix	brain

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