Variant report

Variant	rs11989463
Chromosome Location	chr8:118846051-118846052
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:118845996..118847669-chr8:119122945..119125594,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182197	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10107685	1.00[JPT][hapmap]
rs11562772	1.00[CHB][hapmap]
rs11562773	1.00[CHB][hapmap]
rs11779439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11781699	1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs11996407	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12541615	0.86[AMR][1000 genomes]
rs12541851	1.00[JPT][hapmap]
rs12542013	1.00[JPT][hapmap]
rs12544064	1.00[JPT][hapmap]
rs17430287	0.94[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17431020	1.00[JPT][hapmap]
rs17439693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17450793	1.00[JPT][hapmap]
rs17453176	1.00[JPT][hapmap]
rs17503215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs4345585	1.00[JPT][hapmap]
rs7014925	1.00[CHB][hapmap]
rs72673939	0.86[AMR][1000 genomes]
rs7842361	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831439	chr8:118747352-118899118	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11989463	EXT1	cis	Liver	GTEx
rs11989463	DEPDC6	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118805600-118849800	Strong transcription	Liver	Liver
2	chr8:118808600-118849400	Weak transcription	Stomach Mucosa	stomach
3	chr8:118817200-118852400	Weak transcription	Psoas Muscle	Psoas
4	chr8:118817200-118852400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr8:118819600-118851000	Weak transcription	Fetal Thymus	thymus
6	chr8:118825000-118850000	Weak transcription	Fetal Brain Female	brain
7	chr8:118825200-118848000	Weak transcription	Colonic Mucosa	Colon
8	chr8:118825200-118859600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:118825200-118859800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:118825400-118849200	Weak transcription	Brain Hippocampus Middle	brain
11	chr8:118825400-118849600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:118825400-118852400	Weak transcription	Right Ventricle	heart
13	chr8:118825400-118853200	Weak transcription	Brain Anterior Caudate	brain
14	chr8:118825400-118859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:118825600-118849600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:118825600-118849800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:118825600-118857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:118825600-118860000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:118825800-118846400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:118825800-118850400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:118827200-118847200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr8:118827200-118855000	Weak transcription	Right Atrium	heart
23	chr8:118828600-118857000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:118829200-118847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr8:118829800-118855000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr8:118829800-118859800	Weak transcription	Esophagus	oesophagus
27	chr8:118831200-118846200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr8:118832200-118854800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr8:118832400-118854000	Weak transcription	Gastric	stomach
30	chr8:118832400-118855000	Weak transcription	Colon Smooth Muscle	Colon
31	chr8:118832600-118854400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr8:118832600-118855000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr8:118832600-118859800	Weak transcription	Spleen	Spleen
34	chr8:118833000-118855000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr8:118833200-118847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:118833200-118854600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr8:118834000-118851600	Weak transcription	Fetal Brain Male	brain
38	chr8:118834200-118847600	Weak transcription	Lung	lung
39	chr8:118834800-118851800	Weak transcription	Placenta	Placenta
40	chr8:118835000-118847800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:118835000-118859600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr8:118835000-118859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr8:118837200-118848800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:118837800-118849600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:118838400-118849000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:118838800-118846200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr8:118840600-118846400	Genic enhancers	NHDF-Ad	bronchial
48	chr8:118840600-118846800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:118840800-118848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr8:118841200-118855000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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