Variant report

Variant	rs17285260
Chromosome Location	chr2:172195421-172195422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10460358	0.84[ASW][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap]
rs10930473	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11677562	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11679641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12465868	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]
rs12469151	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12471094	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12616940	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1558963	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs1921776	0.84[ASW][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs2356709	0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4667685	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55862836	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62181358	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62183460	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66893860	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747400	0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs727231	0.96[MEX][hapmap]
rs7590275	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17285260	GAD1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:172176200-172198600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:172180000-172195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:172180600-172203400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:172180800-172198200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:172181000-172203800	Weak transcription	HMEC	breast
8	chr2:172181000-172221600	Weak transcription	K562	blood
9	chr2:172181200-172198000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:172181200-172204200	Weak transcription	NHEK	skin
11	chr2:172183800-172197200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:172184000-172195800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:172184000-172197800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:172184000-172198000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:172184000-172203400	Weak transcription	NH-A	brain
16	chr2:172184600-172203200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:172184800-172195600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:172184800-172195800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:172184800-172203200	Weak transcription	Fetal Thymus	thymus
20	chr2:172184800-172203200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:172185000-172200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:172185000-172202200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:172187000-172204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:172187600-172203000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:172189400-172204200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:172191000-172203200	Weak transcription	Left Ventricle	heart
27	chr2:172191600-172203400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:172193400-172195800	Enhancers	GM12878-XiMat	blood
29	chr2:172193400-172198000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:172193600-172218200	Weak transcription	HepG2	liver
31	chr2:172193800-172203400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:172194000-172200600	Weak transcription	Primary B cells from cord blood	blood
33	chr2:172194200-172203000	Weak transcription	A549	lung

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