Variant report

Variant	rs673869
Chromosome Location	chr11:93540001-93540002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93539702..93541221-chr11:93572458..93574620,2	K562	blood:
2	chr11:93533093..93534985-chr11:93538831..93540954,2	K562	blood:
3	chr11:93525238..93528220-chr11:93538387..93540576,2	K562	blood:

Variant related genes	Relation type
ENSG00000265292	Chromatin interaction
ENSG00000042429	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10741476	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10765633	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10831102	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11020505	0.96[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11020506	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11020507	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11020510	0.84[EUR][1000 genomes]
rs11020521	0.98[EUR][1000 genomes]
rs11020522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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]
rs12292460	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1284102	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1284108	0.96[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1284141	0.81[AMR][1000 genomes]
rs1428919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1783938	0.85[EUR][1000 genomes]
rs2434984	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2848477	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132750	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132751	0.84[EUR][1000 genomes]
rs4753103	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56364420	0.86[EUR][1000 genomes]
rs585713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs586293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs588644	0.85[EUR][1000 genomes]
rs595650	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs598376	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs598427	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601711	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602242	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs602665	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs602703	0.83[ASN][1000 genomes]
rs606087	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs606286	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs606357	0.85[EUR][1000 genomes]
rs606462	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs606749	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs607615	0.85[EUR][1000 genomes]
rs611762	0.84[EUR][1000 genomes]
rs616876	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs618801	0.86[EUR][1000 genomes]
rs621355	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs622147	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs624856	0.83[EUR][1000 genomes]
rs625249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625359	0.82[ASN][1000 genomes]
rs628661	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs628665	0.87[ASN][1000 genomes]
rs630811	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631177	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631261	0.87[ASN][1000 genomes]
rs631705	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs640379	0.85[EUR][1000 genomes]
rs640382	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs640864	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs644009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs644535	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs652621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652961	0.96[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs653939	0.86[EUR][1000 genomes]
rs655158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs655699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.99[ASN][1000 genomes]
rs658181	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs658698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658797	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs659877	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs662070	0.84[EUR][1000 genomes]
rs665507	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs666074	0.81[ASN][1000 genomes]
rs666136	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs670871	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs675441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675501	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs676586	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs681321	0.85[EUR][1000 genomes]
rs687042	0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs687507	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs688634	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs693947	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7943266	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7943525	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7950574	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs673869	GPR83	cis	cerebellum	SCAN
rs673869	SNORD5	cis	cerebellum	SCAN
rs673869	C11orf54	cis	Esophagus Mucosa	GTEx
rs673869	C11orf54	cis	Muscle Skeletal	GTEx
rs673869	C11orf54	cis	Adipose Subcutaneous	GTEx
rs673869	C11orf54	cis	multi-tissue	Pritchard
rs673869	SNORA8	cis	cerebellum	SCAN
rs673869	C11orf54	cis	cerebellum	SCAN
rs673869	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs673869	C11orf54	cis	Artery Aorta	GTEx
rs673869	C11orf54	cis	uninvolved skin	skin_eQTL
rs673869	FUT4	cis	cerebellum	SCAN
rs673869	C11orf54	cis	normal skin	skin_eQTL
rs673869	C11orf54	cis	parietal	SCAN
rs673869	MED17	cis	cerebellum	SCAN
rs673869	C11orf54	cis	Nerve Tibial	GTEx
rs673869	ENDOD1	cis	cerebellum	SCAN
rs673869	C11orf54	cis	lesional skin	skin_eQTL
rs673869	C11orf54	cis	Esophagus Muscularis	GTEx
rs673869	C11orf54	cis	Artery Tibial	GTEx
rs673869	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs673869	C11orf54	cis	lymphoblastoid	seeQTL
rs673869	SCARNA9	cis	parietal	SCAN
rs673869	MED17	cis	parietal	SCAN
rs673869	C11orf54	cis	Heart Left Ventricle	GTEx
rs673869	C11orf54	cis	lung	GTEx
rs673869	C11orf54	cis	Stomach	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93519200-93542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:93520200-93549400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:93520200-93551000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:93520400-93549200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:93520400-93549400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:93520600-93548200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:93520600-93551000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:93520800-93549000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:93520800-93549200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:93520800-93549200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:93520800-93549400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:93520800-93549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:93520800-93549400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:93521000-93547800	Strong transcription	Hela-S3	cervix
15	chr11:93521000-93548600	Strong transcription	NH-A	brain
16	chr11:93521000-93549200	Strong transcription	Fetal Thymus	thymus
17	chr11:93521000-93549600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr11:93521000-93549600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:93521000-93550800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:93521200-93540400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:93521200-93547800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:93521200-93548800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:93521200-93549200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr11:93521200-93549200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:93521200-93549200	Strong transcription	Fetal Intestine Large	intestine
26	chr11:93521200-93549200	Strong transcription	Placenta	Placenta
27	chr11:93521200-93549200	Strong transcription	HUVEC	blood vessel
28	chr11:93521200-93549400	Strong transcription	Primary B cells from cord blood	blood
29	chr11:93521200-93549800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:93521400-93546000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:93521400-93547800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr11:93521400-93549000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:93521400-93549400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:93521400-93549400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:93521400-93549400	Strong transcription	Liver	Liver
36	chr11:93521400-93549400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr11:93521400-93549600	Strong transcription	Adipose Nuclei	Adipose
38	chr11:93521400-93551200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:93521600-93549400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:93521800-93548000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:93521800-93551000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:93522000-93549200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:93522200-93548000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:93522200-93549400	Strong transcription	Primary T cells from cord blood	blood
45	chr11:93522400-93549000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:93522400-93549200	Strong transcription	GM12878-XiMat	blood
47	chr11:93522800-93548400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:93522800-93549200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:93523000-93548600	Strong transcription	Dnd41	blood
50	chr11:93523000-93549200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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