Variant report

Variant	rs12543242
Chromosome Location	chr8:120930025-120930026
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	chr8:120922845..120924939-chr8:120927936..120930832,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10099088	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12541326	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12545586	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13265513	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13265734	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13278508	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13280041	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16893299	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1879149	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2002377	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2017310	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2056305	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2139430	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2139431	0.82[AMR][1000 genomes]
rs2176750	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2326432	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28461628	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28546392	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28600928	0.82[AMR][1000 genomes]
rs4871786	0.82[AMR][1000 genomes]
rs4871793	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4871795	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62528673	0.81[AMR][1000 genomes]
rs6469875	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6469876	0.82[AMR][1000 genomes]
rs6999911	0.82[AFR][1000 genomes]
rs7000068	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7000488	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7004324	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7005888	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7007672	0.83[AFR][1000 genomes]
rs7018038	0.82[AMR][1000 genomes]
rs7462839	0.82[AFR][1000 genomes]
rs7813430	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs869340	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs869341	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9297607	0.82[AMR][1000 genomes]
rs9987135	0.82[AMR][1000 genomes]
rs9987139	0.81[AMR][1000 genomes]
rs9987140	0.82[AMR][1000 genomes]
rs9987142	0.82[AMR][1000 genomes]
rs9987165	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9987297	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
6	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv972194	chr8:120898451-120965081	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1018953	chr8:120910380-120954832	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12543242	DSCC1	cis	Esophagus Muscularis	GTEx
rs12543242	DSCC1	cis	Nerve Tibial	GTEx
rs12543242	DSCC1	cis	Artery Tibial	GTEx
rs12543242	DSCC1	cis	Adipose Subcutaneous	GTEx
rs12543242	DSCC1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120920800-120932800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr8:120921800-120931800	Weak transcription	HSMMtube	muscle
3	chr8:120922000-120931200	Enhancers	Psoas Muscle	Psoas
4	chr8:120923000-120935400	Enhancers	Stomach Mucosa	stomach
5	chr8:120923600-120932800	Weak transcription	Lung	lung
6	chr8:120924000-120931800	Weak transcription	Right Atrium	heart
7	chr8:120925000-120931800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr8:120925000-120932400	Weak transcription	Right Ventricle	heart
9	chr8:120925000-120932600	Weak transcription	Esophagus	oesophagus
10	chr8:120925200-120931800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr8:120925200-120932600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:120925800-120931200	Weak transcription	Brain Anterior Caudate	brain
13	chr8:120926000-120931200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:120926200-120930200	Weak transcription	Fetal Thymus	thymus
15	chr8:120926200-120930400	Weak transcription	Brain Angular Gyrus	brain
16	chr8:120926200-120931000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr8:120926200-120931800	Weak transcription	Placenta	Placenta
18	chr8:120926200-120932600	Weak transcription	Gastric	stomach
19	chr8:120926200-120944400	Weak transcription	Primary T cells from cord blood	blood
20	chr8:120927000-120933000	Enhancers	HepG2	liver
21	chr8:120927000-120934000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:120927200-120931800	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr8:120927200-120933200	Enhancers	Fetal Intestine Large	intestine
24	chr8:120927400-120933400	Enhancers	Fetal Intestine Small	intestine
25	chr8:120927600-120933000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr8:120927600-120933000	Enhancers	Duodenum Mucosa	Duodenum
27	chr8:120927600-120933200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr8:120927800-120931000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr8:120927800-120931600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:120928000-120931200	Weak transcription	Adipose Nuclei	Adipose
31	chr8:120928000-120931800	Weak transcription	Fetal Kidney	kidney
32	chr8:120928000-120931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr8:120928200-120931400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:120928400-120933600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:120928600-120930200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:120928600-120930200	Enhancers	Fetal Stomach	stomach
37	chr8:120928600-120930400	Enhancers	Fetal Lung	lung
38	chr8:120928600-120930600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr8:120928600-120930600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:120928600-120933000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr8:120928600-120933200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr8:120928600-120933400	Enhancers	Fetal Muscle Leg	muscle
43	chr8:120928800-120930200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:120928800-120930200	Enhancers	Brain Substantia Nigra	brain
45	chr8:120928800-120931800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr8:120928800-120933200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr8:120929200-120930600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr8:120929200-120931200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr8:120929400-120930400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:120929400-120930600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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