Variant report

Variant	rs56344213
Chromosome Location	chr5:9553868-9553869
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	chr5:9552447..9554138-chr5:9558237..9561822,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10462868	0.96[ASN][1000 genomes]
rs11749803	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398337	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1508798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614229	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1651285	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1651286	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1706987	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1706992	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs268555	0.85[ASN][1000 genomes]
rs268556	0.85[ASN][1000 genomes]
rs374218	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798099	0.85[ASN][1000 genomes]
rs414396	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs414829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422309	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs431288	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432989	0.85[ASN][1000 genomes]
rs456885	0.85[ASN][1000 genomes]
rs460234	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461337	0.85[ASN][1000 genomes]
rs461750	0.83[ASN][1000 genomes]
rs464621	0.85[ASN][1000 genomes]
rs60322708	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605126	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73051829	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv881586	chr5:9549386-9578794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs56344213	CTD-2001E22.2	cis	Heart Left Ventricle	GTEx
rs56344213	CTD-2001E22.2	cis	Stomach	GTEx
rs56344213	CTD-2001E22.2	cis	Nerve Tibial	GTEx
rs56344213	CTD-2001E22.2	cis	lung	GTEx
rs56344213	CTD-2001E22.2	cis	Esophagus Mucosa	GTEx
rs56344213	CTD-2001E22.2	cis	Muscle Skeletal	GTEx
rs56344213	CTD-2001E22.2	cis	Adipose Subcutaneous	GTEx
rs56344213	CTD-2001E22.2	cis	Artery Aorta	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9547000-9554200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:9548200-9554000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:9548200-9554200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:9548200-9556200	Weak transcription	Right Ventricle	heart
5	chr5:9548200-9558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:9548200-9558400	Weak transcription	Liver	Liver
7	chr5:9548400-9558400	Weak transcription	Fetal Heart	heart
8	chr5:9548600-9558400	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:9549000-9554000	Strong transcription	Fetal Muscle Leg	muscle
10	chr5:9550200-9554400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:9550200-9558400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:9550200-9563000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:9550400-9554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:9550600-9558400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:9550800-9557400	Weak transcription	NHEK	skin
16	chr5:9551200-9554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:9551200-9557400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:9551200-9558200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:9551200-9562200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:9551600-9561800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:9552000-9559200	Weak transcription	Colonic Mucosa	Colon
22	chr5:9552200-9554600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:9552200-9557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:9552200-9557200	Weak transcription	NHLF	lung
25	chr5:9552200-9557400	Weak transcription	HMEC	breast
26	chr5:9552200-9557800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:9552200-9564600	Weak transcription	Aorta	Aorta
28	chr5:9552400-9554000	Weak transcription	Placenta	Placenta
29	chr5:9552400-9557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:9552600-9554200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:9552600-9555000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr5:9552800-9554600	Enhancers	Stomach Mucosa	stomach
33	chr5:9552800-9557200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:9552800-9557200	Weak transcription	Osteobl	bone
35	chr5:9552800-9557400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:9552800-9557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:9552800-9557800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:9552800-9558000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:9552800-9562400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:9552800-9578400	Weak transcription	Ovary	ovary
41	chr5:9553000-9554600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:9553000-9554600	Enhancers	Fetal Intestine Large	intestine
43	chr5:9553000-9554600	Enhancers	Fetal Intestine Small	intestine
44	chr5:9553000-9554800	Enhancers	Duodenum Mucosa	Duodenum
45	chr5:9553000-9556800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:9553000-9557400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:9553000-9560000	Weak transcription	Fetal Lung	lung
48	chr5:9553000-9562200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:9553200-9554000	Enhancers	Esophagus	oesophagus
50	chr5:9553200-9557000	Weak transcription	NH-A	brain

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