Variant report

Variant	rs524281
Chromosome Location	chr11:65886662-65886663
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65842058..65844229-chr11:65885606..65887262,2	MCF-7	breast:
2	chr11:65879652..65882394-chr11:65882531..65887079,5	K562	blood:
3	chr11:65885486..65887843-chr11:65890510..65893124,3	MCF-7	breast:
4	chr11:65836821..65841267-chr11:65881295..65888359,12	MCF-7	breast:
5	chr11:65847868..65850346-chr11:65885324..65888259,3	MCF-7	breast:
6	chr11:65847681..65850551-chr11:65884444..65887331,2	MCF-7	breast:
7	chr11:65836711..65839156-chr11:65879952..65887031,7	MCF-7	breast:
8	chr11:65778443..65780993-chr11:65885172..65889100,3	MCF-7	breast:
9	chr11:65885627..65887432-chr11:65890839..65893836,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1055615	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10791853	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10791856	0.88[ASN][1000 genomes]
rs10896092	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896095	0.84[ASN][1000 genomes]
rs10896097	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227426	0.87[ASN][1000 genomes]
rs12049852	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1717671	0.88[ASN][1000 genomes]
rs1987678	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270448	0.84[TSI][hapmap]
rs2452681	0.82[MEX][hapmap]
rs3088328	0.86[ASN][1000 genomes]
rs471484	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs475805	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs485857	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488320	0.90[ASN][1000 genomes]
rs489337	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs527897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535395	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537497	0.87[GIH][hapmap]
rs539046	0.81[GIH][hapmap]
rs547087	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564343	0.87[GIH][hapmap]
rs565198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs571434	0.92[ASN][1000 genomes]
rs580891	0.86[ASN][1000 genomes]
rs7937281	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7941469	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7942894	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs524281	BATF	trans	lymphoblastoid	seeQTL
rs524281	KLC2	cis	Muscle Skeletal	GTEx
rs524281	RP11-867O8.5	cis	Artery Aorta	GTEx
rs524281	WDR74	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65868600-65893800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:65875000-65887200	Weak transcription	Fetal Muscle Leg	muscle
3	chr11:65876800-65888400	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:65879400-65889400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:65880000-65887000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:65880400-65905000	Weak transcription	Fetal Stomach	stomach
7	chr11:65880600-65894400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:65881000-65886800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:65881000-65892000	Weak transcription	Brain Anterior Caudate	brain
10	chr11:65881000-65894600	Weak transcription	Gastric	stomach
11	chr11:65881400-65888600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:65881600-65893800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:65883400-65886800	Weak transcription	Fetal Kidney	kidney
14	chr11:65883800-65886800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:65883800-65886800	Weak transcription	Adipose Nuclei	Adipose
16	chr11:65883800-65887000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:65883800-65887000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:65883800-65887200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65883800-65887600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:65883800-65888800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:65883800-65894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65884000-65890400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:65884000-65893400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:65884200-65888600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:65884200-65890200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:65884200-65894200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:65884400-65887000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:65884600-65888200	Enhancers	GM12878-XiMat	blood
29	chr11:65884600-65889800	Enhancers	Primary T cells from cord blood	blood
30	chr11:65884600-65890400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:65884600-65893600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:65884600-65893600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:65884800-65888800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:65884800-65889200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:65885000-65893000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr11:65885400-65886800	Enhancers	NH-A	brain
37	chr11:65885400-65887200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:65885400-65887400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:65885400-65887600	Enhancers	HSMM	muscle
40	chr11:65885400-65888000	Enhancers	Osteobl	bone
41	chr11:65885400-65888800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:65885400-65888800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:65885600-65887000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr11:65885600-65887400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr11:65885600-65887600	Enhancers	NHDF-Ad	bronchial
46	chr11:65885600-65887800	Enhancers	Left Ventricle	heart
47	chr11:65885600-65888200	Enhancers	HUVEC	blood vessel
48	chr11:65885600-65888600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:65885600-65892800	Weak transcription	Primary B cells from cord blood	blood
50	chr11:65885600-65893000	Weak transcription	Primary monocytes fromperipheralblood	blood

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