Variant report

Variant	rs10767679
Chromosome Location	chr11:3911216-3911217
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3880021..3883743-chr11:3910117..3913050,3	K562	blood:
2	chr11:3904375..3907098-chr11:3909715..3912468,3	K562	blood:
3	chr11:3899401..3901421-chr11:3909382..3911737,2	K562	blood:
4	chr11:3909574..3911315-chr11:3913084..3915868,2	K562	blood:

Variant related genes	Relation type
ENSG00000230593	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10160254	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160331	0.99[ASN][1000 genomes]
rs10160415	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10160703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160753	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767684	0.99[ASN][1000 genomes]
rs10767685	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10835217	0.88[ASN][1000 genomes]
rs10835226	0.99[ASN][1000 genomes]
rs10835231	0.99[ASN][1000 genomes]
rs10835232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835238	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835239	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835245	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835246	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835247	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835248	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835252	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10835256	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10835261	0.96[ASN][1000 genomes]
rs10835262	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030122	0.89[ASN][1000 genomes]
rs11030176	0.99[ASN][1000 genomes]
rs11030209	1.00[JPT][hapmap]
rs11030211	0.85[JPT][hapmap]
rs12275981	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869084	0.90[CHD][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs1869085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs1964492	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4414209	0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4598668	0.85[JPT][hapmap]
rs4622250	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4910584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7113148	1.00[JPT][hapmap]
rs7118295	0.98[ASN][1000 genomes]
rs7120336	0.99[ASN][1000 genomes]
rs7126870	0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs7131437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7131469	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	esv275356	chr11:3908738-3913014	Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10767679	TRIM22	cis	parietal	SCAN
rs10767679	FAM160A2	cis	cerebellum	SCAN
rs10767679	OR56A1	cis	parietal	SCAN
rs10767679	OR56A5	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3889200-3913400	Weak transcription	Aorta	Aorta
2	chr11:3891400-3915000	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:3899200-3926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:3899800-3915600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:3900000-3916000	Weak transcription	Spleen	Spleen
6	chr11:3901200-3914600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:3902000-3911400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:3902200-3914600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:3902200-3916400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:3902200-3916400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:3902400-3916400	Weak transcription	Fetal Intestine Small	intestine
12	chr11:3902400-3923800	Weak transcription	Gastric	stomach
13	chr11:3905800-3915200	Weak transcription	Esophagus	oesophagus
14	chr11:3905800-3915200	Weak transcription	Right Ventricle	heart
15	chr11:3906000-3913000	Weak transcription	Small Intestine	intestine
16	chr11:3906000-3914200	Weak transcription	Primary T cells from cord blood	blood
17	chr11:3906000-3914600	Enhancers	Primary B cells from cord blood	blood
18	chr11:3906000-3915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:3906000-3915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:3907000-3913200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:3907200-3912200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:3907200-3915600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:3907400-3914600	Weak transcription	Osteobl	bone
24	chr11:3907400-3915400	Weak transcription	Lung	lung
25	chr11:3907400-3915600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:3907400-3923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:3907600-3915400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:3907600-3922600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:3907800-3915200	Weak transcription	HMEC	breast
30	chr11:3908000-3912000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr11:3908200-3914000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr11:3908400-3911400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:3908400-3912400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr11:3909600-3911400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:3909600-3914400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:3909600-3915600	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:3909800-3911600	Weak transcription	Left Ventricle	heart
38	chr11:3909800-3914000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr11:3909800-3914200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:3910000-3912600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:3910000-3913000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr11:3910000-3913600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:3910000-3914000	Weak transcription	Fetal Thymus	thymus
44	chr11:3910200-3913400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr11:3910200-3914000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:3910200-3914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:3910200-3914400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:3910200-3915000	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:3910400-3911400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:3910400-3911400	Weak transcription	GM12878-XiMat	blood

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