Variant report

Variant	rs6434401
Chromosome Location	chr2:191469192-191469193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191464759..191466338-chr2:191468193..191471068,2	K562	blood:
2	chr2:191398124..191401338-chr2:191468460..191472195,4	K562	blood:

Variant related genes	Relation type
ENSG00000233654	Chromatin interaction
ENSG00000189362	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10169169	0.81[EUR][1000 genomes]
rs10171376	0.88[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	0.98[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];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs10209340	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs10737936	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11553601	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs13006708	0.84[AFR][1000 genomes]
rs13031452	0.81[EUR][1000 genomes]
rs13384743	0.82[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs13386210	0.82[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];1.00[GIH][hapmap];0.85[TSI][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];0.84[GIH][hapmap]
rs13412663	0.82[CHB][hapmap]
rs13417310	0.81[EUR][1000 genomes]
rs13418943	0.80[EUR][1000 genomes]
rs13429315	0.80[EUR][1000 genomes]
rs28452331	0.84[AFR][1000 genomes]
rs3811608	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs4283453	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs4853712	0.82[CHB][hapmap]
rs4853719	0.98[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]
rs6434403	0.92[YRI][hapmap]
rs6706036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711561	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741118	0.98[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];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs7564107	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7574844	0.81[EUR][1000 genomes]
rs7584379	0.81[EUR][1000 genomes]
rs7594994	0.80[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];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs9967829	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]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6434401	MFSD6	cis	lymphoblastoid	seeQTL
rs6434401	NAB1	cis	Esophagus Mucosa	GTEx
rs6434401	TMEM194B	cis	cerebellum	SCAN
rs6434401	MFSD6	cis	parietal	SCAN
rs6434401	FLJ20160	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 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	chr2:191463800-191470600	Weak transcription	HMEC	breast
6	chr2:191464800-191471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:191464800-191471800	Weak transcription	Right Atrium	heart
8	chr2:191464800-191472000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:191465000-191471800	Weak transcription	Right Ventricle	heart
10	chr2:191465400-191470000	Weak transcription	Primary T cells from cord blood	blood
11	chr2:191465600-191471600	Weak transcription	HSMMtube	muscle
12	chr2:191467000-191469600	Enhancers	Brain Angular Gyrus	brain
13	chr2:191467200-191469400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:191467200-191470000	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:191467200-191470000	Enhancers	Brain Hippocampus Middle	brain
16	chr2:191467400-191469400	Enhancers	A549	lung
17	chr2:191468000-191473200	Enhancers	Fetal Heart	heart
18	chr2:191468200-191471600	Weak transcription	NHLF	lung
19	chr2:191468400-191471200	Weak transcription	Left Ventricle	heart
20	chr2:191468800-191469400	Enhancers	Brain Anterior Caudate	brain
21	chr2:191468800-191469400	Enhancers	Brain Substantia Nigra	brain
22	chr2:191468800-191470800	Enhancers	Hela-S3	cervix
23	chr2:191469000-191469200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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