Variant report

Variant	rs11030976
Chromosome Location	chr11:4129859-4129860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:4122423..4125552-chr11:4126686..4130745,3	K562	blood:
2	chr11:4122423..4125513-chr11:4126686..4130996,4	K562	blood:
3	chr11:4124837..4126563-chr11:4128507..4131052,2	MCF-7	breast:
4	chr11:4118205..4121110-chr11:4126914..4129955,3	K562	blood:

Variant related genes	Relation type
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10835613	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835650	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030907	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11030967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030980	0.88[AMR][1000 genomes]
rs11031043	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11031096	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11604649	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12292367	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12364664	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12803023	0.88[CHD][hapmap]
rs1372805	0.81[ASW][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap]
rs1662172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662173	0.83[AMR][1000 genomes]
rs183484	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1980412	0.86[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs2119986	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284452	0.83[AMR][1000 genomes]
rs2304891	0.81[ASW][hapmap];0.82[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs232054	0.83[AMR][1000 genomes]
rs2412344	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2735689	0.83[AMR][1000 genomes]
rs2735691	0.86[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2920144	0.81[ASW][hapmap];0.81[CHD][hapmap]
rs2959068	0.88[CHD][hapmap]
rs3794049	0.83[AMR][1000 genomes]
rs54816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67074167	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110060	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7124301	0.82[EUR][1000 genomes]
rs725518	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747883	0.83[EUR][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	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	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
3	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
4	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
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11030976	TRIM5	cis	cerebellum	SCAN
rs11030976	RRM1	cis	Artery Tibial	GTEx
rs11030976	OR51E2	cis	cerebellum	SCAN
rs11030976	RRM1	cis	cerebellum	SCAN
rs11030976	KRTAP5-4	cis	cerebellum	SCAN
rs11030976	OR52I2	cis	parietal	SCAN
rs11030976	TRIM21	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117000-4137200	Weak transcription	Esophagus	oesophagus
2	chr11:4117000-4141000	Weak transcription	Ovary	ovary
3	chr11:4117200-4142200	Weak transcription	Colonic Mucosa	Colon
4	chr11:4117400-4141800	Weak transcription	Small Intestine	intestine
5	chr11:4117600-4133000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:4117600-4137400	Weak transcription	Right Ventricle	heart
7	chr11:4117600-4144600	Weak transcription	HSMMtube	muscle
8	chr11:4117600-4145200	Weak transcription	Gastric	stomach
9	chr11:4117600-4153000	Weak transcription	Stomach Mucosa	stomach
10	chr11:4117800-4147800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:4118400-4146400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:4118400-4156200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:4118800-4141000	Weak transcription	Brain Germinal Matrix	brain
16	chr11:4119000-4137800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:4119400-4157600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:4121000-4159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:4121600-4142800	Weak transcription	Fetal Brain Male	brain
20	chr11:4122000-4139800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:4122400-4158000	Strong transcription	Dnd41	blood
22	chr11:4122800-4135200	Strong transcription	Hela-S3	cervix
23	chr11:4122800-4136800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:4122800-4141800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:4122800-4158000	Strong transcription	Fetal Thymus	thymus
26	chr11:4123000-4135200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:4123000-4135600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:4123000-4136000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:4123000-4138200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:4123000-4152000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:4123000-4157600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:4123000-4157600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr11:4123000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:4123200-4130800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr11:4123200-4135600	Strong transcription	Placenta	Placenta
36	chr11:4123200-4136600	Strong transcription	Osteobl	bone
37	chr11:4123200-4158000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr11:4123800-4135000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:4123800-4135400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr11:4124000-4157600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:4124000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:4124400-4138200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:4124600-4138000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:4124800-4138200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:4125200-4138000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:4125400-4137400	Weak transcription	Pancreas	Pancrea
47	chr11:4125800-4130200	Strong transcription	Primary hematopoietic stem cells	blood
48	chr11:4125800-4130200	Strong transcription	HUVEC	blood vessel
49	chr11:4126000-4142000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:4126200-4131400	Strong transcription	Fetal Lung	lung

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