Variant report

Variant	rs11164963
Chromosome Location	chr1:94146121-94146122
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94146007..94146592-chr1:94279239..94279807,2	MCF-7	breast:
2	chr1:94096921..94097933-chr1:94146005..94146828,3	MCF-7	breast:
3	chr1:94094810..94095721-chr1:94145946..94146885,3	MCF-7	breast:
4	chr1:94144888..94147261-chr1:94311172..94313468,2	K562	blood:
5	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:
6	chr1:94145935..94146771-chr11:66056379..66057009,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000174851	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1011903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12079723	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084853	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1567791	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236284	0.87[CEU][hapmap]
rs236287	0.87[CEU][hapmap]
rs236344	0.80[MEX][hapmap]
rs423493	0.80[MEX][hapmap]
rs61781002	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6660740	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701871	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6702036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704479	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7513130	0.85[CEU][hapmap]
rs7519952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs955470	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9659100	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh 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
rs11164963	SNORD21	cis	cerebellum	SCAN
rs11164963	F3	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94140200-94146200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:94141000-94146200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94141400-94146200	Weak transcription	Aorta	Aorta
4	chr1:94143800-94146200	Transcr. at gene 5' and 3'	HMEC	breast
5	chr1:94143800-94146600	Transcr. at gene 5' and 3'	NHEK	skin
6	chr1:94144400-94146400	Flanking Active TSS	HUVEC	blood vessel
7	chr1:94144400-94148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:94144600-94146200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:94144600-94148400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:94144800-94146200	Weak transcription	Small Intestine	intestine
11	chr1:94144800-94146400	Flanking Active TSS	NHLF	lung
12	chr1:94144800-94146400	Flanking Active TSS	Osteobl	bone
13	chr1:94145000-94146400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:94145000-94146600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:94145000-94148000	Active TSS	Brain Anterior Caudate	brain
16	chr1:94145200-94146400	Flanking Active TSS	HSMMtube	muscle
17	chr1:94145200-94148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:94145400-94147600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr1:94145400-94147800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:94145400-94148400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:94145400-94148400	Active TSS	HSMM	muscle
22	chr1:94145600-94146200	Enhancers	Stomach Mucosa	stomach
23	chr1:94145600-94146400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:94145600-94146400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:94145600-94147600	Active TSS	Fetal Kidney	kidney
26	chr1:94145600-94147800	Active TSS	NHDF-Ad	bronchial
27	chr1:94145600-94148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:94145600-94148200	Active TSS	A549	lung
29	chr1:94145800-94146200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
30	chr1:94145800-94146200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:94145800-94146200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
32	chr1:94145800-94146200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:94145800-94146200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
34	chr1:94145800-94146200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr1:94145800-94146200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:94145800-94146200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:94145800-94146200	Enhancers	Primary B cells from cord blood	blood
38	chr1:94145800-94146200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:94145800-94146200	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr1:94145800-94146200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr1:94145800-94146200	Flanking Active TSS	Esophagus	oesophagus
42	chr1:94145800-94146200	Flanking Active TSS	Placenta	Placenta
43	chr1:94145800-94146200	Flanking Active TSS	Left Ventricle	heart
44	chr1:94145800-94146200	Flanking Active TSS	Lung	lung
45	chr1:94145800-94146200	Flanking Active TSS	Psoas Muscle	Psoas
46	chr1:94145800-94146200	Active TSS	Stomach Smooth Muscle	stomach
47	chr1:94145800-94146200	Enhancers	K562	blood
48	chr1:94145800-94146400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:94145800-94146400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
50	chr1:94145800-94146400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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