Variant report

Variant	rs12465868
Chromosome Location	chr2:172212652-172212653
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	chr2:172211606..172213974-chr2:172215315..172217354,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10460358	0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs10930473	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11677562	1.00[JPT][hapmap]
rs11679641	1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12469151	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12471094	1.00[JPT][hapmap]
rs12616940	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1558963	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17285260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1921776	0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2356709	0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4667685	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55862836	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62181358	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62183460	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66893860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747400	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs727231	0.96[MEX][hapmap]
rs7590275	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12465868	GAD1	cis	cerebellum	SCAN
rs12465868	C1orf115	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:172181000-172221600	Weak transcription	K562	blood
3	chr2:172193600-172218200	Weak transcription	HepG2	liver
4	chr2:172203400-172217200	Weak transcription	Small Intestine	intestine
5	chr2:172203800-172218600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:172204000-172213800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:172204600-172218600	Weak transcription	Ovary	ovary
8	chr2:172204800-172222400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:172205000-172213000	Weak transcription	A549	lung
10	chr2:172205000-172215200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:172205000-172216600	Weak transcription	Adipose Nuclei	Adipose
12	chr2:172205000-172217200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:172205000-172221400	Weak transcription	NHEK	skin
14	chr2:172205000-172221600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:172205000-172221800	Weak transcription	Osteobl	bone
16	chr2:172205000-172222400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:172205200-172218400	Weak transcription	Psoas Muscle	Psoas
18	chr2:172205200-172218400	Weak transcription	NHDF-Ad	bronchial
19	chr2:172205200-172221600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:172205200-172224000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:172211600-172214800	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr2:172211600-172215000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr2:172211600-172216000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:172211800-172213600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
26	chr2:172211800-172215000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr2:172211800-172215000	ZNF genes & repeats	Fetal Stomach	stomach
28	chr2:172211800-172215200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:172211800-172215600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:172211800-172217000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:172212200-172214600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr2:172212200-172215400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr2:172212400-172213200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr2:172212400-172214200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:172212400-172214200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:172212400-172221600	Weak transcription	HMEC	breast
37	chr2:172212400-172222400	Weak transcription	Aorta	Aorta
38	chr2:172212400-172231400	Weak transcription	Esophagus	oesophagus
39	chr2:172212600-172213400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:172212600-172214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:172212600-172214600	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr2:172212600-172215600	ZNF genes & repeats	GM12878-XiMat	blood

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