Variant report

Variant	rs2568090
Chromosome Location	chr11:8849495-8849496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8847275..8850671-chr11:8853327..8856938,3	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10769947	0.81[CEU][hapmap]
rs10769948	0.81[CEU][hapmap]
rs10769957	0.81[CEU][hapmap]
rs10769958	0.90[CHB][hapmap]
rs10769967	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10769968	0.82[EUR][1000 genomes]
rs10769970	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769971	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769979	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs10840130	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10840134	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840141	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840142	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs10840148	1.00[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs11042059	0.81[CEU][hapmap]
rs11042078	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042079	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042082	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042088	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042102	0.84[EUR][1000 genomes]
rs11042103	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11042125	0.86[MEX][hapmap]
rs11042149	0.81[CEU][hapmap]
rs11042151	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs11042154	0.93[CEU][hapmap]
rs1123936	0.85[CEU][hapmap]
rs11603841	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12224436	0.81[CEU][hapmap]
rs12421789	0.91[CHB][hapmap]
rs12794444	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529641	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1560569	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs1569408	0.82[EUR][1000 genomes]
rs1883098	0.82[EUR][1000 genomes]
rs1980428	0.85[CEU][hapmap]
rs1980429	0.84[CEU][hapmap]
rs1988708	0.82[EUR][1000 genomes]
rs1988709	0.84[EUR][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs2292049	0.87[CHD][hapmap]
rs2316865	0.81[CEU][hapmap]
rs2568025	0.84[CHD][hapmap]
rs2568031	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2568032	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2568043	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568045	0.85[CEU][hapmap]
rs2568054	0.82[EUR][1000 genomes]
rs2568059	0.84[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs2568062	0.83[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs2653567	0.82[EUR][1000 genomes]
rs2653570	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs2653593	0.83[EUR][1000 genomes]
rs2653605	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs2653606	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653607	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653616	0.83[EUR][1000 genomes]
rs2653617	0.80[YRI][hapmap]
rs2742480	0.84[CEU][hapmap]
rs2742536	0.85[CEU][hapmap]
rs2742537	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2742540	0.92[CEU][hapmap];0.82[MEX][hapmap]
rs2742545	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs2742550	0.83[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs34842234	0.83[EUR][1000 genomes]
rs3763918	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs4554887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4579928	0.91[CHB][hapmap]
rs4909952	0.92[CEU][hapmap]
rs4910062	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910442	0.84[CEU][hapmap]
rs4929911	0.81[CEU][hapmap]
rs4929912	0.81[CEU][hapmap]
rs4929914	0.81[CEU][hapmap]
rs4929922	0.82[MEX][hapmap]
rs61876187	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7119939	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7123861	0.84[EUR][1000 genomes]
rs7479407	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs7925728	0.93[CEU][hapmap]
rs7930026	0.92[CEU][hapmap]
rs7937298	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7943377	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945705	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7947631	0.85[CEU][hapmap]
rs891787	0.80[YRI][hapmap]
rs905290	0.80[CEU][hapmap]
rs978636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3372624	chr11:8848476-8852774	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2568090	OR51B6	cis	parietal	SCAN
rs2568090	TRIM22	cis	parietal	SCAN
rs2568090	OR51Q1	cis	parietal	SCAN
rs2568090	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2568090	ST5	cis	parietal	SCAN
rs2568090	AKIP1	cis	Thyroid	GTEx
rs2568090	APBB1	cis	parietal	SCAN
rs2568090	WEE1	cis	parietal	SCAN
rs2568090	TMEM9B	cis	parietal	SCAN
rs2568090	MRVI1	cis	cerebellum	SCAN
rs2568090	NRIP3	cis	parietal	SCAN
rs2568090	C11orf17	cis	cerebellum	SCAN
rs2568090	OR51A7	cis	cerebellum	SCAN
rs2568090	TMEM9B-AS1	cis	lung	GTEx
rs2568090	OR52A1	cis	parietal	SCAN
rs2568090	RRP8	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
2	chr11:8836400-8849800	Weak transcription	Fetal Intestine Small	intestine
3	chr11:8836600-8850400	Weak transcription	Fetal Lung	lung
4	chr11:8837000-8850000	Weak transcription	Lung	lung
5	chr11:8839200-8849600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:8845200-8854200	Weak transcription	Psoas Muscle	Psoas
7	chr11:8845800-8860000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:8846600-8854400	Weak transcription	Fetal Intestine Large	intestine
9	chr11:8847000-8852800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:8847200-8849800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr11:8847200-8849800	Enhancers	NHLF	lung
12	chr11:8847400-8850400	Enhancers	K562	blood
13	chr11:8847600-8849600	Enhancers	Placenta	Placenta
14	chr11:8847600-8850400	Enhancers	Ovary	ovary
15	chr11:8847600-8852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:8848000-8849600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:8848000-8850200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:8848000-8850400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr11:8848000-8852800	Enhancers	Fetal Thymus	thymus
20	chr11:8848200-8849600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr11:8848200-8853400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:8848400-8849600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr11:8848400-8850400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:8848400-8850400	Weak transcription	Fetal Kidney	kidney
25	chr11:8848400-8850400	Enhancers	HSMMtube	muscle
26	chr11:8848400-8850800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr11:8848600-8849600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:8848600-8849600	Weak transcription	Brain Anterior Caudate	brain
29	chr11:8848600-8850800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:8848600-8850800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr11:8848800-8849800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:8848800-8849800	Enhancers	Spleen	Spleen
33	chr11:8848800-8850200	Enhancers	HSMM	muscle
34	chr11:8848800-8852200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:8848800-8852400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:8848800-8853000	Weak transcription	HMEC	breast
37	chr11:8849000-8849800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:8849000-8849800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:8849000-8849800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:8849000-8850200	Weak transcription	Osteobl	bone
41	chr11:8849000-8850400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:8849000-8850400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr11:8849000-8850600	Weak transcription	Esophagus	oesophagus
44	chr11:8849000-8852600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:8849000-8852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:8849000-8853000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:8849000-8853800	Genic enhancers	Fetal Muscle Leg	muscle
48	chr11:8849000-8854000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:8849000-8854000	Strong transcription	Fetal Stomach	stomach
50	chr11:8849000-8854000	Weak transcription	Stomach Mucosa	stomach

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