Variant report

Variant	rs7940013
Chromosome Location	chr11:4138304-4138305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr11:4138242-4138330	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:4131355..4133542-chr11:4137072..4140145,3	K562	blood:

Variant related genes	Relation type
RRM1	TF binding region
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10742242	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10767845	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835596	0.84[CHD][hapmap]
rs10835611	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835684	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835719	0.84[TSI][hapmap]
rs11030639	0.82[CHD][hapmap]
rs11030781	0.82[CHD][hapmap]
rs11030918	0.83[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs11031110	0.95[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12290828	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806698	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs2044135	0.84[TSI][hapmap]
rs2056853	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165728	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268168	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284450	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34832073	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35359151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817657	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910599	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910886	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910888	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910889	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910904	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7111104	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7130580	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7932702	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7949663	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs963998	0.82[CHD][hapmap]
rs9666229	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9666857	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv1048590	chr11:4133055-4225100	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv540911	chr11:4133055-4225100	Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1053482	chr11:4138062-4276133	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7940013	TRIM5	cis	cerebellum	SCAN
rs7940013	RRM1	cis	Artery Tibial	GTEx
rs7940013	IFITM5	cis	cerebellum	SCAN
rs7940013	TRIM21	cis	cerebellum	SCAN
rs7940013	RRM1	cis	cerebellum	SCAN
rs7940013	RRM1	cis	multi-tissue	Pritchard
rs7940013	ANO9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117000-4141000	Weak transcription	Ovary	ovary
2	chr11:4117200-4142200	Weak transcription	Colonic Mucosa	Colon
3	chr11:4117400-4141800	Weak transcription	Small Intestine	intestine
4	chr11:4117600-4144600	Weak transcription	HSMMtube	muscle
5	chr11:4117600-4145200	Weak transcription	Gastric	stomach
6	chr11:4117600-4153000	Weak transcription	Stomach Mucosa	stomach
7	chr11:4117800-4147800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:4118400-4146400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:4118400-4156200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:4118800-4141000	Weak transcription	Brain Germinal Matrix	brain
13	chr11:4119400-4157600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:4121000-4159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:4121600-4142800	Weak transcription	Fetal Brain Male	brain
16	chr11:4122000-4139800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:4122400-4158000	Strong transcription	Dnd41	blood
18	chr11:4122800-4141800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:4122800-4158000	Strong transcription	Fetal Thymus	thymus
20	chr11:4123000-4152000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:4123000-4157600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:4123000-4157600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:4123000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:4123200-4158000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:4124000-4157600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:4124000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:4126000-4142000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:4126600-4166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:4127000-4151000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:4127400-4138600	Weak transcription	NHLF	lung
31	chr11:4127400-4142200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:4127400-4148400	Weak transcription	Psoas Muscle	Psoas
33	chr11:4127600-4141600	Weak transcription	Aorta	Aorta
34	chr11:4127600-4144400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:4127600-4144400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:4127600-4158000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:4129000-4140000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:4130200-4144600	Weak transcription	Fetal Heart	heart
39	chr11:4131000-4138400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:4131000-4138400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:4131000-4150400	Strong transcription	Primary T cells from cord blood	blood
42	chr11:4131000-4157400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:4132200-4151600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr11:4132400-4141400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:4133400-4140000	Weak transcription	NHEK	skin
46	chr11:4133400-4140400	Weak transcription	Fetal Brain Female	brain
47	chr11:4133400-4141600	Weak transcription	Brain Substantia Nigra	brain
48	chr11:4133400-4141800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:4133600-4141400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:4134200-4144400	Weak transcription	Placenta Amnion	Placenta Amnion

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