Variant report

Variant	rs12201249
Chromosome Location	chr6:25625736-25625737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25623561..25626504-chr6:25628972..25630630,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456322	1.00[JPT][hapmap]
rs10456323	1.00[JPT][hapmap]
rs10456325	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12191432	1.00[JPT][hapmap]
rs12192331	1.00[JPT][hapmap]
rs12192342	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12195457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12207791	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12208868	1.00[JPT][hapmap]
rs12214693	0.81[ASN][1000 genomes]
rs12216281	0.86[ASN][1000 genomes]
rs1410443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs150533	1.00[JPT][hapmap]
rs184202	1.00[JPT][hapmap]
rs1883257	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs212927	1.00[JPT][hapmap]
rs212929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs212931	1.00[JPT][hapmap]
rs212932	1.00[JPT][hapmap]
rs212935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs212937	1.00[JPT][hapmap]
rs212939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs212940	1.00[JPT][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs485567	1.00[JPT][hapmap]
rs55633691	0.81[ASN][1000 genomes]
rs55883446	0.81[ASN][1000 genomes]
rs56383372	0.81[ASN][1000 genomes]
rs6902158	1.00[JPT][hapmap]
rs6913169	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918563	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927384	1.00[JPT][hapmap]
rs6931843	1.00[JPT][hapmap]
rs72839082	0.81[ASN][1000 genomes]
rs72839085	0.81[ASN][1000 genomes]
rs72839087	0.81[ASN][1000 genomes]
rs72839088	0.81[ASN][1000 genomes]
rs72839089	0.81[ASN][1000 genomes]
rs72840515	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72840523	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72840524	0.86[ASN][1000 genomes]
rs72840525	0.86[ASN][1000 genomes]
rs7741026	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742338	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9348685	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9379774	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9461190	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9467544	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467555	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12201249	LRRC16	cis	lesional skin	skin_eQTL
rs12201249	LRRC16	cis	normal skin	skin_eQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
4	chr6:25594200-25629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:25594400-25627200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:25594600-25627200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:25594600-25629600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:25595000-25626800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:25595000-25627000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:25601600-25626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:25609400-25627000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:25612800-25626800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:25613200-25631000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:25619200-25625800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:25619800-25628600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:25622800-25626400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:25622800-25626400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:25622800-25627600	Weak transcription	Aorta	Aorta
19	chr6:25622800-25634800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:25623000-25627200	Weak transcription	Primary T cells from cord blood	blood
21	chr6:25623400-25627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:25624200-25626800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:25624600-25626400	Enhancers	HepG2	liver
24	chr6:25625200-25630600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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