Variant report

Variant	rs13057617
Chromosome Location	chr22:34247064-34247065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34245347..34248923-chr22:34315491..34319689,7	MCF-7	breast:
2	chr22:34246562..34250566-chr22:34253925..34258689,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133424	Chromatin interaction
ENSG00000273082	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1009730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13056358	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13058568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547409	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1807710	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2018292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227023	1.00[CHD][hapmap]
rs238857	1.00[CHD][hapmap]
rs28374	1.00[CHD][hapmap]
rs34780334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35709129	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs496956	1.00[CHB][hapmap]
rs5754679	1.00[CHD][hapmap]
rs8138735	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9607079	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9607080	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9607086	0.86[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9609876	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609877	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609878	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609879	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv529886	chr22:34153740-34258847	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13057617	LARGE	cis	cerebellum	SCAN
rs13057617	KREMEN1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34237800-34247200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr22:34238400-34249000	Weak transcription	Aorta	Aorta
3	chr22:34240600-34247200	Weak transcription	Right Atrium	heart
4	chr22:34240800-34247400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:34240800-34247400	Weak transcription	Colon Smooth Muscle	Colon
6	chr22:34242200-34247600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:34243200-34248800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr22:34243200-34250800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr22:34243800-34248000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:34244000-34247600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr22:34244600-34247200	Weak transcription	HSMM	muscle
12	chr22:34244600-34249000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr22:34244800-34247200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr22:34244800-34247200	Weak transcription	Lung	lung
15	chr22:34244800-34249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:34245000-34247200	Weak transcription	Osteobl	bone
17	chr22:34245200-34247200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:34245400-34247400	Weak transcription	GM12878-XiMat	blood
19	chr22:34245800-34249600	Enhancers	Fetal Intestine Large	intestine
20	chr22:34246000-34247800	Enhancers	Small Intestine	intestine
21	chr22:34246000-34248400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr22:34246000-34248600	Enhancers	Fetal Lung	lung
23	chr22:34246000-34249600	Enhancers	Fetal Intestine Small	intestine
24	chr22:34246200-34247800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr22:34246200-34247800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr22:34246200-34248000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr22:34246200-34249000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr22:34246200-34249200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:34246200-34249200	Enhancers	Duodenum Mucosa	Duodenum
30	chr22:34246200-34249200	Enhancers	Stomach Mucosa	stomach
31	chr22:34246200-34249600	Enhancers	Fetal Heart	heart
32	chr22:34246400-34247400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr22:34246400-34247400	Weak transcription	Ovary	ovary
34	chr22:34246400-34248600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:34246400-34249000	Weak transcription	Brain Angular Gyrus	brain
36	chr22:34246400-34249200	Weak transcription	Pancreas	Pancrea
37	chr22:34246600-34247800	Enhancers	Left Ventricle	heart
38	chr22:34246600-34248200	Enhancers	Brain Germinal Matrix	brain
39	chr22:34246800-34247200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr22:34246800-34247400	Enhancers	Gastric	stomach
41	chr22:34246800-34247400	Enhancers	NHDF-Ad	bronchial
42	chr22:34246800-34248200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr22:34246800-34248400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr22:34246800-34249200	Enhancers	NHLF	lung
45	chr22:34246800-34249400	Enhancers	Psoas Muscle	Psoas
46	chr22:34246800-34249600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:34247000-34247200	Enhancers	Spleen	Spleen
48	chr22:34247000-34247400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
49	chr22:34247000-34247400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr22:34247000-34247400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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