Variant report

Variant	rs11998247
Chromosome Location	chr8:120960219-120960220
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:120954144..120956394-chr8:120958181..120960542,2	K562	blood:
2	chr8:120959692..120962314-chr8:121016213..121017926,2	MCF-7	breast:
3	chr8:120954144..120956709-chr8:120959042..120961843,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10087605	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10099088	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10102995	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11984773	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11984866	1.00[CEU][hapmap]
rs12548248	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12677306	0.86[CEU][hapmap]
rs12679478	0.91[CEU][hapmap]
rs13265513	0.87[CEU][hapmap]
rs16893299	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1879149	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2056305	0.87[CEU][hapmap]
rs2326432	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4073559	0.95[CEU][hapmap]
rs4871010	0.95[CEU][hapmap]
rs4871011	0.95[CEU][hapmap]
rs4871786	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4871793	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4871795	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs55660329	0.88[ASN][1000 genomes]
rs6469866	0.87[CEU][hapmap]
rs6469875	0.87[CEU][hapmap]
rs6469876	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs68097758	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6995862	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6996081	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs7005888	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs7018038	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7388491	0.95[CEU][hapmap]
rs7813263	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs7813430	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7823280	0.95[CEU][hapmap]
rs869340	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs869341	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9649948	0.95[CEU][hapmap]
rs9987135	1.00[JPT][hapmap]
rs9987139	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs9987140	0.90[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	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
8	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11998247	DEPDC6	cis	cerebellum	SCAN
rs11998247	DEPDC6	cis	lesional skin	skin_eQTL
rs11998247	DSCC1	cis	cerebellum	SCAN
rs11998247	DSCC1	cis	parietal	SCAN
rs11998247	DEPDC6	cis	uninvolved skin	skin_eQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120935800-120963200	Weak transcription	Psoas Muscle	Psoas
2	chr8:120945200-120977400	Weak transcription	Fetal Kidney	kidney
3	chr8:120947400-120963200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr8:120947400-120964400	Weak transcription	Adipose Nuclei	Adipose
5	chr8:120947400-120968000	Weak transcription	Spleen	Spleen
6	chr8:120951600-120963400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr8:120954000-120960400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr8:120954200-120968000	Weak transcription	Stomach Mucosa	stomach
9	chr8:120954600-120970400	Weak transcription	Fetal Stomach	stomach
10	chr8:120954800-120964400	Weak transcription	Right Atrium	heart
11	chr8:120955400-120963600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr8:120955600-120963600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:120956400-120960600	Enhancers	Brain Angular Gyrus	brain
14	chr8:120956400-120960600	Enhancers	Brain Hippocampus Middle	brain
15	chr8:120956600-120963000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr8:120958400-120960400	Enhancers	Brain Substantia Nigra	brain
17	chr8:120958800-120960600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr8:120959000-120960400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr8:120959000-120960400	Enhancers	Stomach Smooth Muscle	stomach
20	chr8:120959200-120960400	Enhancers	Brain Cingulate Gyrus	brain
21	chr8:120959200-120960400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:120959200-120960400	Enhancers	Rectal Smooth Muscle	rectum
23	chr8:120959400-120960400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:120959400-120960400	Enhancers	Duodenum Mucosa	Duodenum
25	chr8:120959400-120960400	Enhancers	Left Ventricle	heart
26	chr8:120959600-120960400	Enhancers	Fetal Intestine Small	intestine
27	chr8:120959600-120960600	Enhancers	Brain Anterior Caudate	brain
28	chr8:120959600-120963400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr8:120959600-120964400	Weak transcription	Fetal Muscle Leg	muscle
30	chr8:120959600-120968600	Weak transcription	Aorta	Aorta
31	chr8:120959800-120960400	Enhancers	Colon Smooth Muscle	Colon
32	chr8:120959800-120966400	Weak transcription	Ovary	ovary
33	chr8:120959800-120977400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr8:120960000-120960400	Strong transcription	Liver	Liver
35	chr8:120960000-120960400	Enhancers	Gastric	stomach
36	chr8:120960000-120960400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr8:120960000-120960600	Enhancers	Fetal Intestine Large	intestine
38	chr8:120960000-120968600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:120960200-120960400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr8:120960200-120960600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr8:120960200-120964000	Weak transcription	Primary hematopoietic stem cells	blood

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