Variant report

Variant	rs6487271
Chromosome Location	chr12:22222883-22222884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12423101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423142	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424838	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578369	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs12816385	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12818845	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12827678	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2193379	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2418036	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487278	0.97[ASN][1000 genomes]
rs67339960	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71448623	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300481	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969132	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7978726	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]

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	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758298	chr12:22140834-22339299	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2759883	chr12:22140834-22736907	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv438196	chr12:22195202-22234058	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1850259	chr12:22198865-22244741	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6487271	TTTY6	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22202200-22223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:22203800-22235200	Weak transcription	Gastric	stomach
3	chr12:22204600-22223400	Weak transcription	Pancreas	Pancrea
4	chr12:22209800-22223200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:22209800-22229200	Weak transcription	Thymus	Thymus
6	chr12:22216200-22233200	Weak transcription	K562	blood
7	chr12:22218800-22223000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:22219200-22223000	Weak transcription	Placenta	Placenta
9	chr12:22219600-22224200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:22220000-22223600	Weak transcription	Fetal Lung	lung
11	chr12:22220400-22223000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:22220400-22223200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:22221200-22223000	Weak transcription	Liver	Liver
14	chr12:22222000-22224400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:22222200-22223400	Enhancers	Fetal Intestine Small	intestine
16	chr12:22222200-22224600	Enhancers	Fetal Intestine Large	intestine
17	chr12:22222800-22223200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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

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