Variant report

Variant	rs149957
Chromosome Location	chr6:28037020-28037021
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28031578..28034623-chr6:28036187..28038874,3	K562	blood:
2	chr6:28035744..28039366-chr6:28039863..28043405,5	K562	blood:
3	chr6:28036286..28038554-chr6:28302021..28304261,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000220721	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1150672	0.82[AFR][1000 genomes]
rs1150674	0.86[AFR][1000 genomes]
rs1150676	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1150680	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs1150683	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1150684	0.88[AFR][1000 genomes]
rs1225593	0.92[YRI][hapmap]
rs1225594	0.86[AFR][1000 genomes]
rs1225709	0.82[ASW][hapmap];0.87[TSI][hapmap]
rs1225711	0.88[AFR][1000 genomes]
rs1233784	0.88[AFR][1000 genomes]
rs1237873	1.00[ASW][hapmap];0.87[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs1416997	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1480646	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs149898	0.85[YRI][hapmap]
rs1529749	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs156741	1.00[ASW][hapmap]
rs156742	1.00[ASW][hapmap]
rs1613149	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1619221	0.92[YRI][hapmap]
rs1654777	0.86[AFR][1000 genomes]
rs1654778	0.86[AFR][1000 genomes]
rs169432	1.00[YRI][hapmap]
rs169433	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs172164	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs175955	0.92[YRI][hapmap]
rs1770130	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1770132	1.00[YRI][hapmap]
rs1770133	0.86[AFR][1000 genomes]
rs17709097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17709109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17709523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17765491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1871695	1.00[ASW][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs200959	0.82[ASW][hapmap]
rs200970	1.00[ASW][hapmap]
rs2030008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs203865	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs203868	0.94[AFR][1000 genomes]
rs203870	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs203871	0.85[AFR][1000 genomes]
rs203874	1.00[YRI][hapmap]
rs203875	0.86[AFR][1000 genomes]
rs203881	0.94[AFR][1000 genomes]
rs203885	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs203891	0.88[AFR][1000 genomes]
rs203894	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2394044	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2622318	0.92[YRI][hapmap]
rs2622321	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs276364	1.00[ASW][hapmap]
rs2791334	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs370266	0.88[AFR][1000 genomes]
rs392665	0.88[AFR][1000 genomes]
rs41375446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs425159	0.85[YRI][hapmap]
rs427348	1.00[ASW][hapmap];0.91[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs539474	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs57349346	0.86[AFR][1000 genomes]
rs58909320	0.84[AFR][1000 genomes]
rs73742609	0.88[AFR][1000 genomes]
rs9348782	1.00[JPT][hapmap]
rs9348785	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9348790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9348791	0.94[AFR][1000 genomes]
rs9348795	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9357055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9357056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9357059	0.81[ASN][1000 genomes]
rs9368540	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9368545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9380042	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9393873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9393874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9393879	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[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	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs149957	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28035800-28037200	Enhancers	K562	blood
2	chr6:28036600-28037200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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