Variant report

Variant	rs12788554
Chromosome Location	chr11:86502853-86502854
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	chr11:86336690..86338701-chr11:86502692..86504518,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10501629	1.00[CHB][hapmap]
rs10898531	1.00[CHB][hapmap]
rs10898535	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11234753	1.00[CHB][hapmap]
rs11234765	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11234767	1.00[CHB][hapmap]
rs11234768	1.00[CHB][hapmap]
rs11234778	1.00[CHB][hapmap]
rs11234798	1.00[CHB][hapmap]
rs11234799	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11234804	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11234805	1.00[ASN][1000 genomes]
rs11234806	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11234818	1.00[CHB][hapmap]
rs11602353	1.00[CHB][hapmap]
rs11602721	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604191	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11606902	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607392	1.00[CHB][hapmap]
rs11608167	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12360547	1.00[CHB][hapmap]
rs12362094	1.00[ASN][1000 genomes]
rs12786875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs12787853	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs12791740	1.00[CHB][hapmap]
rs12793595	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12799567	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805405	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159941	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758195	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758206	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758334	1.00[CHB][hapmap]
rs17758376	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758400	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17820139	1.00[CHB][hapmap]
rs1815753	1.00[CHB][hapmap]
rs1939118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000537	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186617	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34873514	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781614	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592313	1.00[CHB][hapmap]
rs6592314	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7105597	1.00[CHB][hapmap]
rs7128682	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7128805	1.00[CHB][hapmap]
rs750789	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754490	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872619	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86495400-86510400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:86497000-86510000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:86500000-86506400	Enhancers	Hela-S3	cervix
4	chr11:86501400-86503400	Enhancers	Fetal Lung	lung
5	chr11:86501600-86503600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:86501800-86503000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:86502000-86503400	Enhancers	Ovary	ovary
8	chr11:86502000-86503600	Enhancers	Fetal Muscle Leg	muscle
9	chr11:86502000-86503600	Enhancers	Psoas Muscle	Psoas
10	chr11:86502000-86503600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr11:86502000-86503600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr11:86502000-86505600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:86502200-86503600	Enhancers	Pancreas	Pancrea
14	chr11:86502200-86505400	Weak transcription	A549	lung
15	chr11:86502400-86509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:86502400-86510800	Weak transcription	Fetal Intestine Large	intestine
17	chr11:86502600-86503000	Enhancers	Stomach Smooth Muscle	stomach
18	chr11:86502600-86506400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:86502600-86511000	Weak transcription	Fetal Kidney	kidney
20	chr11:86502800-86505600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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