Variant report

Variant	rs6486379
Chromosome Location	chr11:17551191-17551192
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17550003..17552043-chr11:17563166..17565257,2	K562	blood:
2	chr11:17099359..17101768-chr11:17550989..17553473,2	K562	blood:
3	chr11:17536439..17538354-chr11:17550411..17553263,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006611	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10766409	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832797	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024319	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041027	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237956	0.86[ASN][1000 genomes]
rs2237957	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237959	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486378	0.89[ASN][1000 genomes]
rs7111978	0.89[AFR][1000 genomes]
rs7125811	0.80[AFR][1000 genomes]
rs732983	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878546	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878547	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6486379	USH1C	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
4	chr11:17540800-17552400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:17541000-17552600	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr11:17541400-17552400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:17541600-17551600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:17545400-17553000	Weak transcription	Gastric	stomach
10	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
11	chr11:17549000-17553400	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:17549200-17551400	Enhancers	HSMMtube	muscle
13	chr11:17549400-17552600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr11:17549600-17551200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:17549600-17551600	Enhancers	Brain Anterior Caudate	brain
16	chr11:17549600-17551800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr11:17549600-17553000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr11:17549600-17553800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:17549800-17551200	Enhancers	Fetal Heart	heart
20	chr11:17549800-17552600	Weak transcription	Colonic Mucosa	Colon
21	chr11:17549800-17553400	Enhancers	Fetal Brain Male	brain
22	chr11:17550000-17551400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr11:17550000-17552000	Enhancers	Brain Substantia Nigra	brain
24	chr11:17550000-17552400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:17550000-17553800	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr11:17550200-17551800	Enhancers	Fetal Muscle Trunk	muscle
27	chr11:17550200-17552800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:17550400-17551600	Strong transcription	Fetal Intestine Large	intestine
29	chr11:17550400-17552600	Weak transcription	Spleen	Spleen
30	chr11:17550600-17551200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:17550800-17551400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:17550800-17551400	Bivalent Enhancer	Fetal Stomach	stomach
33	chr11:17550800-17551600	Enhancers	Brain Angular Gyrus	brain
34	chr11:17550800-17552600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:17550800-17552600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:17551000-17551200	Enhancers	Brain Germinal Matrix	brain
37	chr11:17551000-17551200	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr11:17551000-17551200	Bivalent Enhancer	HSMM	muscle
39	chr11:17551000-17551600	Flanking Active TSS	Fetal Brain Female	brain
40	chr11:17551000-17551800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:17551000-17552600	Weak transcription	Right Atrium	heart

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