Variant report

Variant	rs7312135
Chromosome Location	chr12:48085848-48085849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48079504..48082471-chr12:48085134..48087838,3	K562	blood:
2	chr12:48085079..48087645-chr12:48089413..48091227,2	K562	blood:
3	chr12:48085007..48087672-chr12:48089308..48092914,4	K562	blood:

Variant related genes	Relation type
ENSG00000005175	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082722	0.88[EUR][1000 genomes]
rs10083203	0.88[EUR][1000 genomes]
rs1046438	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875668	0.88[EUR][1000 genomes]
rs10875672	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875675	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875678	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168172	0.88[EUR][1000 genomes]
rs11168174	0.86[EUR][1000 genomes]
rs11168189	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168210	0.83[ASN][1000 genomes]
rs11503868	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11534912	0.89[EUR][1000 genomes]
rs11559971	0.87[ASN][1000 genomes]
rs12301106	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12318569	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233051	0.83[ASN][1000 genomes]
rs1237844	0.93[CHB][hapmap]
rs2022528	0.88[EUR][1000 genomes]
rs2057730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239187	0.81[ASW][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs2285831	0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs2524319	0.83[ASN][1000 genomes]
rs3809318	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768840	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768841	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768842	0.85[ASN][1000 genomes]
rs56009115	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294629	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298493	0.88[EUR][1000 genomes]
rs73102109	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73104122	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113128	0.88[EUR][1000 genomes]
rs7314657	0.88[EUR][1000 genomes]
rs74088008	0.88[ASN][1000 genomes]
rs7960755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929269	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs9668083	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7312135	SLC38A4	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
3	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
5	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:48046600-48099200	Weak transcription	Gastric	stomach
8	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
11	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
12	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
13	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
15	chr12:48058200-48086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:48058800-48086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48060600-48086000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:48060600-48094200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:48060800-48094200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:48061600-48088600	Weak transcription	Brain Substantia Nigra	brain
22	chr12:48062600-48094200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:48062800-48098600	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:48063000-48086400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
26	chr12:48064600-48086000	Weak transcription	Lung	lung
27	chr12:48064600-48086000	Weak transcription	HSMMtube	muscle
28	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:48064800-48089600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:48064800-48090000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:48065000-48092800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:48066400-48086000	Weak transcription	Fetal Heart	heart
33	chr12:48068400-48097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:48071800-48091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:48072800-48086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:48072800-48090200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:48072800-48091400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:48072800-48091600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:48073000-48091800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:48073200-48086600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:48073600-48091200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:48074000-48093600	Weak transcription	HMEC	breast
43	chr12:48074000-48095400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:48074000-48095800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr12:48074200-48097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:48074200-48099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr12:48075000-48086000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:48075600-48086000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:48075600-48086000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:48075600-48087800	Weak transcription	Brain Anterior Caudate	brain

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