Variant report

Variant	rs2300231
Chromosome Location	chr12:12315880-12315881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12315377..12318046-chr12:12335015..12337960,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015830	0.93[ASN][1000 genomes]
rs10743981	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1074992	0.94[CEU][hapmap]
rs10845498	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs10845504	0.93[CEU][hapmap]
rs11054697	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11054701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11054752	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1181333	0.83[AFR][1000 genomes]
rs12318846	0.84[AFR][1000 genomes]
rs12580417	0.84[EUR][1000 genomes]
rs1468878	0.81[AFR][1000 genomes]
rs16907786	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907810	0.92[ASW][hapmap];0.94[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2075241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2160521	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2160589	0.92[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3825258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265667	0.85[EUR][1000 genomes]
rs4619236	0.92[CEU][hapmap]
rs4763789	0.84[EUR][1000 genomes]
rs61130413	0.85[AFR][1000 genomes]
rs7134001	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7313285	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7968660	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2300231	M6PR	cis	cerebellum	SCAN
rs2300231	DERA	cis	parietal	SCAN
rs2300231	MANSC1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
7	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:12288200-12342800	Weak transcription	K562	blood
9	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:12297600-12321400	Weak transcription	Gastric	stomach
12	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
13	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:12302800-12317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:12303600-12318200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:12303800-12316200	Weak transcription	GM12878-XiMat	blood
18	chr12:12303800-12316600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
20	chr12:12304000-12319800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:12305400-12317400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:12305400-12318000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:12306600-12318200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:12306800-12325200	Weak transcription	Small Intestine	intestine
26	chr12:12307800-12317600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:12309600-12318000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:12310000-12321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:12311200-12317400	Weak transcription	Fetal Brain Male	brain
30	chr12:12312000-12317400	Weak transcription	Brain Angular Gyrus	brain
31	chr12:12312000-12317400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:12312000-12317400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:12312000-12325000	Weak transcription	Aorta	Aorta
34	chr12:12312000-12325000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:12312000-12332600	Weak transcription	Dnd41	blood
36	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:12312200-12316600	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:12312200-12316800	Weak transcription	Left Ventricle	heart
39	chr12:12312200-12317000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:12312200-12317000	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:12312200-12317400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:12312200-12325000	Weak transcription	HMEC	breast
43	chr12:12312200-12334000	Weak transcription	Pancreas	Pancrea
44	chr12:12312200-12334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
46	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
48	chr12:12312400-12319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:12312400-12325200	Weak transcription	Primary T cells from cord blood	blood
50	chr12:12312400-12332400	Weak transcription	Primary hematopoietic stem cells	blood

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