Variant report

Variant	rs11679641
Chromosome Location	chr2:172232319-172232320
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
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];0.95[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.80[ASN][1000 genomes]
rs10930473	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11677562	0.95[JPT][hapmap];0.89[YRI][hapmap]
rs12465868	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	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12471094	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12616940	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1558963	0.91[JPT][hapmap];1.00[MEX][hapmap]
rs17285260	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]
rs1921776	0.84[ASW][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs2356709	0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4667685	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55862836	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62181358	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62183460	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66893860	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747400	0.91[JPT][hapmap];1.00[MEX][hapmap]
rs727231	1.00[MEX][hapmap]
rs7590275	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[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	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
3	nsv979147	chr2:172227772-172232665	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11679641	GAD1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172222200-172289600	Weak transcription	Gastric	stomach
3	chr2:172222400-172240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:172223000-172235400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:172223000-172242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:172229400-172246800	Weak transcription	NH-A	brain
7	chr2:172230600-172233000	ZNF genes & repeats	GM12878-XiMat	blood
8	chr2:172231400-172232600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr2:172231400-172233200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:172231400-172248000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:172231600-172232800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr2:172231800-172239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:172231800-172240800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:172231800-172243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:172231800-172248200	Weak transcription	Esophagus	oesophagus
16	chr2:172232000-172253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:172232200-172232400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:172232200-172238800	Weak transcription	Liver	Liver
19	chr2:172232200-172242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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