Variant report

Variant	rs5749682
Chromosome Location	chr22:34248314-34248315
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:34245347..34248923-chr22:34315491..34319689,7	MCF-7	breast:
2	chr22:34248240..34252170-chr22:34315347..34319641,4	MCF-7	breast:
3	chr22:34247996..34248570-chr22:34261032..34261815,2	MCF-7	breast:
4	chr22:34247616..34248584-chr22:34315645..34316533,2	MCF-7	breast:
5	chr22:34248231..34249994-chr22:34261049..34263874,2	MCF-7	breast:
6	chr22:34246562..34250566-chr22:34253925..34258689,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273082	Chromatin interaction
ENSG00000133424	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10854636	0.89[AFR][1000 genomes]
rs10854637	0.89[AFR][1000 genomes]
rs10854638	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10854639	0.89[AFR][1000 genomes]
rs10854640	0.89[AFR][1000 genomes]
rs12159281	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12484737	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs16993156	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17809399	1.00[ASW][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2018285	0.94[CEU][hapmap];0.83[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2253063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267306	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[ASN][1000 genomes]
rs2267307	1.00[YRI][hapmap]
rs2283952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749677	0.81[JPT][hapmap]
rs5749679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749680	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754715	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5754716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5754731	0.89[GIH][hapmap]
rs5999121	1.00[YRI][hapmap]
rs5999123	1.00[ASW][hapmap];0.97[GIH][hapmap];1.00[YRI][hapmap]
rs738949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8135968	1.00[YRI][hapmap]

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
rs5749682	HSCB	cis	parietal	SCAN
rs5749682	CABP7	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34238400-34249000	Weak transcription	Aorta	Aorta
2	chr22:34243200-34248800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr22:34243200-34250800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr22:34244600-34249000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:34244800-34249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:34245800-34249600	Enhancers	Fetal Intestine Large	intestine
7	chr22:34246000-34248400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr22:34246000-34248600	Enhancers	Fetal Lung	lung
9	chr22:34246000-34249600	Enhancers	Fetal Intestine Small	intestine
10	chr22:34246200-34249000	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr22:34246200-34249200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr22:34246200-34249200	Enhancers	Duodenum Mucosa	Duodenum
13	chr22:34246200-34249200	Enhancers	Stomach Mucosa	stomach
14	chr22:34246200-34249600	Enhancers	Fetal Heart	heart
15	chr22:34246400-34248600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:34246400-34249000	Weak transcription	Brain Angular Gyrus	brain
17	chr22:34246400-34249200	Weak transcription	Pancreas	Pancrea
18	chr22:34246800-34248400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:34246800-34249200	Enhancers	NHLF	lung
20	chr22:34246800-34249400	Enhancers	Psoas Muscle	Psoas
21	chr22:34246800-34249600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr22:34247000-34248400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:34247000-34249400	Enhancers	Rectal Smooth Muscle	rectum
24	chr22:34247000-34249600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr22:34247200-34248600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr22:34247200-34249200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr22:34247200-34249200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr22:34247200-34249400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:34247200-34249400	Weak transcription	Spleen	Spleen
30	chr22:34247400-34248400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr22:34247400-34248400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr22:34247400-34248400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr22:34247400-34248600	Enhancers	Brain Cingulate Gyrus	brain
34	chr22:34247400-34249200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr22:34247400-34249200	Enhancers	Colon Smooth Muscle	Colon
36	chr22:34247400-34249600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr22:34247400-34249600	Weak transcription	Gastric	stomach
38	chr22:34247400-34249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr22:34247400-34250400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr22:34247600-34248400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:34247600-34249400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr22:34247600-34249600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr22:34247600-34249600	Weak transcription	Fetal Brain Female	brain
44	chr22:34247800-34248400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr22:34247800-34248600	Weak transcription	Ovary	ovary
46	chr22:34247800-34249000	Weak transcription	Fetal Kidney	kidney
47	chr22:34247800-34249000	Weak transcription	Left Ventricle	heart
48	chr22:34247800-34249000	Weak transcription	Small Intestine	intestine
49	chr22:34247800-34249200	Enhancers	Colonic Mucosa	Colon
50	chr22:34247800-34249200	Weak transcription	Osteobl	bone

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