Variant report

Variant	rs10742229
Chromosome Location	chr11:4090305-4090306
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3876316..3878234-chr11:4090130..4092439,2	K562	blood:
2	chr11:4086299..4090336-chr11:4101261..4104407,3	K562	blood:
3	chr11:4083954..4086302-chr11:4087607..4091172,3	K562	blood:
4	chr11:4088836..4091273-chr11:4101944..4103940,2	K562	blood:
5	chr11:4088238..4090623-chr11:4092934..4095144,2	K562	blood:

Variant related genes	Relation type
ENSG00000263421	Chromatin interaction
ENSG00000167323	Chromatin interaction
ENSG00000228661	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10742194	0.90[YRI][hapmap]
rs10767827	0.97[YRI][hapmap];0.94[AFR][1000 genomes]
rs11030814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602757	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1442725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465952	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1662163	0.87[CEU][hapmap]
rs1735053	0.87[CEU][hapmap]
rs2060822	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2289570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412341	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs2898950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920137	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920140	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923947	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2923951	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923952	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923954	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959060	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959061	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959064	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959069	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959073	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959076	0.85[CHB][hapmap]
rs35695744	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910595	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910874	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6578440	0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs7109811	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs7924858	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926908	0.81[EUR][1000 genomes]
rs7927493	0.88[EUR][1000 genomes]
rs7930739	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940635	0.84[EUR][1000 genomes]
rs7945918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894457	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9735835	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988893	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
3	chr11:4067800-4093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:4070800-4108600	Weak transcription	HSMM	muscle
5	chr11:4073000-4093200	Weak transcription	Fetal Intestine Small	intestine
6	chr11:4076200-4103000	Weak transcription	Fetal Intestine Large	intestine
7	chr11:4078000-4093200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:4079000-4093000	Weak transcription	Brain Germinal Matrix	brain
9	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
10	chr11:4079800-4093200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:4081000-4101800	Weak transcription	Lung	lung
12	chr11:4081000-4104600	Weak transcription	Colonic Mucosa	Colon
13	chr11:4081200-4093000	Weak transcription	Fetal Kidney	kidney
14	chr11:4081200-4095400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:4081400-4095600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:4081600-4092800	Weak transcription	Fetal Stomach	stomach
17	chr11:4081800-4095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:4081800-4095600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:4082000-4093400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:4082600-4091000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:4082600-4093000	Weak transcription	Placenta	Placenta
22	chr11:4082600-4093200	Weak transcription	Brain Anterior Caudate	brain
23	chr11:4082600-4093400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:4082600-4094800	Weak transcription	Spleen	Spleen
25	chr11:4082600-4107400	Weak transcription	Stomach Mucosa	stomach
26	chr11:4082800-4093600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:4082800-4103400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:4083000-4090800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:4083000-4094200	Weak transcription	K562	blood
30	chr11:4083000-4095000	Weak transcription	HMEC	breast
31	chr11:4083200-4091200	Weak transcription	Liver	Liver
32	chr11:4083200-4093000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:4083200-4102200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:4084200-4095400	Weak transcription	NHEK	skin
35	chr11:4084400-4091600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr11:4085000-4091800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr11:4085000-4093400	Strong transcription	Thymus	Thymus
38	chr11:4085200-4091400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:4085400-4090400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr11:4085400-4091400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:4085400-4091600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:4085400-4091800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:4085600-4090600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr11:4085600-4091000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr11:4085800-4091000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr11:4085800-4091200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr11:4086200-4102600	Weak transcription	Pancreas	Pancrea
48	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
49	chr11:4086400-4094800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:4087200-4091000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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