Variant report

Variant	rs2859354
Chromosome Location	chr6:28459244-28459245
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28457050..28459909-chr6:28532442..28533968,2	K562	blood:
2	chr6:28458124..28459784-chr6:28640264..28642062,2	K562	blood:
3	chr6:28457438..28459900-chr6:28562762..28564476,2	K562	blood:
4	chr6:28457551..28459368-chr6:28582863..28585503,2	K562	blood:
5	chr6:28457441..28459439-chr6:28472256..28474388,2	K562	blood:
6	chr6:28456855..28459742-chr6:28553402..28555898,3	MCF-7	breast:
7	chr6:28364266..28370257-chr6:28453674..28463075,14	K562	blood:
8	chr6:28457939..28459727-chr6:28472888..28474894,2	K562	blood:
9	chr6:28457372..28460097-chr6:28460579..28463613,3	MCF-7	breast:
10	chr6:28458817..28460819-chr6:28647431..28649482,3	K562	blood:
11	chr6:28364227..28369783-chr6:28455559..28460332,7	K562	blood:
12	chr6:28457570..28459445-chr6:28579762..28581303,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000246350	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1015810	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962141	0.86[ASN][1000 genomes]
rs11965542	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966042	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11966237	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966949	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11968771	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969150	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11969304	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970404	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078422	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108924	1.00[CEU][hapmap]
rs213227	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs213235	0.91[EUR][1000 genomes]
rs2159274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531801	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2531802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs2531819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531826	0.91[EUR][1000 genomes]
rs2531828	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs28382592	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859353	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859359	0.91[EUR][1000 genomes]
rs2859362	0.91[EUR][1000 genomes]
rs2859367	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2859371	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859375	1.00[CEU][hapmap]
rs2859376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859377	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859378	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs385908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403774	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423118	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57147168	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58945456	0.86[ASN][1000 genomes]
rs59457415	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60137363	0.86[ASN][1000 genomes]
rs61540948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916243	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6923104	0.86[ASN][1000 genomes]
rs6932394	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719370	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs73385806	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385807	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385810	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385818	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385870	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387810	0.91[EUR][1000 genomes]
rs73391136	1.00[ASN][1000 genomes]
rs73399084	0.91[EUR][1000 genomes]
rs73401012	0.91[EUR][1000 genomes]
rs73401666	0.91[EUR][1000 genomes]
rs73402995	0.86[ASN][1000 genomes]
rs73404956	0.86[ASN][1000 genomes]
rs73404986	0.83[ASN][1000 genomes]
rs73405002	0.86[ASN][1000 genomes]
rs73407126	1.00[ASN][1000 genomes]
rs73409118	0.86[ASN][1000 genomes]
rs73409123	1.00[ASN][1000 genomes]
rs73409134	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739389	0.91[EUR][1000 genomes]
rs7742658	0.86[ASN][1000 genomes]
rs7759845	1.00[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28456400-28459400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:28456400-28460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28458400-28459600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:28458600-28459800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:28458800-28459400	Enhancers	Fetal Thymus	thymus
6	chr6:28458800-28459600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:28458800-28459800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr6:28458800-28459800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:28458800-28459800	Active TSS	K562	blood
10	chr6:28458800-28465600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:28459200-28460000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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