Variant report

Variant	rs9967829
Chromosome Location	chr2:191470703-191470704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:191398808..191400464-chr2:191469531..191472101,2	K562	blood:
2	chr2:191469811..191472994-chr2:191510666..191514604,3	K562	blood:
3	chr2:191464759..191466338-chr2:191468193..191471068,2	K562	blood:
4	chr2:191398124..191401338-chr2:191468460..191472195,4	K562	blood:
5	chr2:191466430..191468300-chr2:191469650..191471465,2	K562	blood:

Variant related genes	Relation type
ENSG00000138386	Chromatin interaction
ENSG00000233654	Chromatin interaction
ENSG00000189362	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10165399	0.83[YRI][hapmap]
rs10169169	0.81[EUR][1000 genomes]
rs10171376	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs10173975	0.81[EUR][1000 genomes]
rs10179262	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs10185147	0.82[CHB][hapmap]
rs10185228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189140	0.81[EUR][1000 genomes]
rs10208737	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs10209340	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs10737936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11553601	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs13031452	0.81[EUR][1000 genomes]
rs13384743	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs13386210	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs13388162	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs13395233	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs13398741	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs13405215	0.81[EUR][1000 genomes]
rs13410179	0.82[CHB][hapmap]
rs13412663	0.82[CHB][hapmap]
rs13417310	0.81[EUR][1000 genomes]
rs13418943	0.80[EUR][1000 genomes]
rs13429315	0.80[EUR][1000 genomes]
rs3811608	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs4283453	0.82[CHB][hapmap]
rs4853712	0.82[CHB][hapmap]
rs4853719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58210597	0.81[EUR][1000 genomes]
rs58253207	0.81[EUR][1000 genomes]
rs6434401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741118	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054092	0.81[EUR][1000 genomes]
rs7556716	0.83[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs7560045	0.81[EUR][1000 genomes]
rs7562013	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs7564107	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs7574844	0.81[EUR][1000 genomes]
rs7584379	0.81[EUR][1000 genomes]
rs7594994	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs7609330	0.83[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs894072	0.82[CHB][hapmap]
rs8962	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs9288174	0.83[CEU][hapmap];0.82[CHB][hapmap]

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	nsv834492	chr2:191438864-191646621	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9967829	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs9967829	FLJ20160	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191456600-191491800	Weak transcription	Aorta	Aorta
2	chr2:191457000-191471600	Weak transcription	Psoas Muscle	Psoas
3	chr2:191462000-191471600	Weak transcription	Fetal Lung	lung
4	chr2:191462000-191471600	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:191464800-191471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:191464800-191471800	Weak transcription	Right Atrium	heart
7	chr2:191464800-191472000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:191465000-191471800	Weak transcription	Right Ventricle	heart
9	chr2:191465600-191471600	Weak transcription	HSMMtube	muscle
10	chr2:191468000-191473200	Enhancers	Fetal Heart	heart
11	chr2:191468200-191471600	Weak transcription	NHLF	lung
12	chr2:191468400-191471200	Weak transcription	Left Ventricle	heart
13	chr2:191468800-191470800	Enhancers	Hela-S3	cervix
14	chr2:191469400-191472200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:191469400-191472200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:191469400-191472600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:191469600-191472600	Weak transcription	Brain Angular Gyrus	brain
18	chr2:191470400-191470800	Enhancers	Fetal Intestine Small	intestine
19	chr2:191470400-191472200	Enhancers	GM12878-XiMat	blood
20	chr2:191470400-191473800	Enhancers	K562	blood
21	chr2:191470400-191480400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:191470600-191470800	Enhancers	Fetal Intestine Large	intestine
23	chr2:191470600-191471000	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:191470600-191471600	Enhancers	A549	lung
25	chr2:191470600-191472600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:191470600-191472600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:191470600-191473400	Enhancers	HMEC	breast

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