Variant report

Variant	rs10769936
Chromosome Location	chr11:8654528-8654529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8653431..8656351-chr11:8659273..8662125,2	K562	blood:
2	chr11:8653142..8657454-chr11:8704411..8706075,3	K562	blood:
3	chr11:8651247..8655516-chr11:8698768..8704091,5	MCF-7	breast:
4	chr11:8625850..8627964-chr11:8654045..8656261,2	K562	blood:
5	chr11:8653441..8656999-chr11:8666272..8669350,3	K562	blood:
6	chr11:8652377..8654542-chr11:8721939..8724339,2	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000254900	Chromatin interaction
ENSG00000200983	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10128597	0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743073	0.84[CEU][hapmap]
rs10769931	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10769932	0.92[ASN][1000 genomes]
rs10769938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769939	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10840099	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10840100	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10840102	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840104	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042016	0.96[ASN][1000 genomes]
rs11042017	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042018	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11042023	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11042025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042029	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042030	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12271470	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12295855	0.84[CEU][hapmap]
rs12575252	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12577287	0.83[CEU][hapmap]
rs12803166	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1502317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867810	0.84[CEU][hapmap]
rs2166470	0.84[CEU][hapmap]
rs2316901	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34867877	0.95[ASN][1000 genomes]
rs35319120	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36092927	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4256980	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4272783	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4291677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4495896	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4503528	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929923	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4929924	0.97[ASN][1000 genomes]
rs4929925	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4929926	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929927	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929928	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929941	0.83[MEX][hapmap]
rs4929947	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs4929948	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6486253	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7110529	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113874	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7118611	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7126235	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7931834	0.84[CEU][hapmap]
rs7939673	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7941510	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950166	0.97[ASN][1000 genomes]
rs7950528	0.94[ASN][1000 genomes]
rs885114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10769936	SNORA45	cis	parietal	SCAN
rs10769936	IPO7	cis	cerebellum	SCAN
rs10769936	TRIM66	cis	Nerve Tibial	GTEx
rs10769936	RPL27A	cis	parietal	SCAN
rs10769936	OR10A4	cis	parietal	SCAN
rs10769936	TRIM66	cis	Whole Blood	GTEx
rs10769936	STK33	cis	cerebellum	SCAN
rs10769936	SNORA45	cis	cerebellum	SCAN
rs10769936	ST5	cis	cerebellum	SCAN
rs10769936	CNGA4	cis	cerebellum	SCAN
rs10769936	TRIM66	cis	Skin Sun Exposed Lower leg	GTEx
rs10769936	RPL27A	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8626000-8661600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:8626000-8661800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:8626800-8659600	Weak transcription	Hela-S3	cervix
4	chr11:8632800-8659000	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:8632800-8663800	Weak transcription	Fetal Kidney	kidney
6	chr11:8634600-8661600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:8634600-8661800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:8634800-8657600	Weak transcription	Psoas Muscle	Psoas
9	chr11:8635400-8661400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:8636200-8661400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:8636600-8657000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:8637000-8661600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
14	chr11:8637400-8659200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:8637800-8657800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:8638400-8657400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:8639600-8661000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:8639800-8659800	Weak transcription	K562	blood
19	chr11:8641400-8661600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:8641800-8666200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:8643400-8658800	Weak transcription	HSMMtube	muscle
22	chr11:8643800-8659200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:8644800-8663400	Weak transcription	Fetal Lung	lung
24	chr11:8644800-8667000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:8645800-8655000	Weak transcription	Fetal Thymus	thymus
26	chr11:8646000-8655000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:8646000-8661600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:8646200-8656200	Weak transcription	A549	lung
29	chr11:8646200-8671000	Weak transcription	HUVEC	blood vessel
30	chr11:8646400-8656000	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:8646400-8666400	Weak transcription	HSMM	muscle
32	chr11:8646600-8654600	Weak transcription	GM12878-XiMat	blood
33	chr11:8646600-8655600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:8646600-8655600	Weak transcription	HepG2	liver
35	chr11:8646600-8656000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:8646600-8656000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:8646600-8656600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:8646600-8656800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:8646800-8655600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:8646800-8655600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:8646800-8655800	Weak transcription	Fetal Intestine Large	intestine
42	chr11:8646800-8656000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:8646800-8656000	Weak transcription	Placenta	Placenta
44	chr11:8646800-8656400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:8646800-8657200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:8646800-8657400	Weak transcription	Left Ventricle	heart
47	chr11:8646800-8657800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:8647000-8655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:8647000-8655000	Weak transcription	Spleen	Spleen
50	chr11:8647000-8655200	Weak transcription	Brain Hippocampus Middle	brain

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