Variant report

Variant	rs11236173
Chromosome Location	chr11:74332262-74332263
allele	A/G
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	POLR2A	chr11:74332197-74332265	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74262725..74264241-chr11:74332037..74334538,2	K562	blood:
2	chr11:74329666..74333357-chr11:74338236..74343135,4	K562	blood:
3	chr11:74331938..74333541-chr11:74336474..74339178,2	MCF-7	breast:

Variant related genes	Relation type
POLD3	TF binding region
ENSG00000077514	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10501417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051058	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10899015	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899018	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899023	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236176	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12288519	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807398	1.00[ASN][1000 genomes]
rs1433970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4145953	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4944051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4944052	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944912	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944913	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944914	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944917	0.97[ASN][1000 genomes]
rs4944922	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4944923	0.94[ASN][1000 genomes]
rs4944925	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4996254	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6592577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7101472	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7106219	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7123887	0.97[ASN][1000 genomes]
rs7130195	0.97[ASN][1000 genomes]
rs7130839	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925556	0.90[ASN][1000 genomes]
rs7936385	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7944208	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11236173	CLPB	cis	parietal	SCAN
rs11236173	RAB6A	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74304400-74345600	Weak transcription	Gastric	stomach
2	chr11:74304600-74345600	Weak transcription	Esophagus	oesophagus
3	chr11:74304600-74373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:74304800-74336200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:74304800-74357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:74304800-74361400	Weak transcription	Colonic Mucosa	Colon
7	chr11:74310200-74352400	Weak transcription	Fetal Brain Male	brain
8	chr11:74311600-74337200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:74311800-74340600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:74314000-74370200	Weak transcription	Psoas Muscle	Psoas
11	chr11:74317200-74345600	Weak transcription	Pancreas	Pancrea
12	chr11:74317200-74352200	Weak transcription	Aorta	Aorta
13	chr11:74317400-74344200	Weak transcription	Small Intestine	intestine
14	chr11:74318600-74334000	Strong transcription	Dnd41	blood
15	chr11:74319200-74334000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:74319200-74366000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr11:74319600-74334200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:74320600-74334000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:74321600-74364800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:74322200-74334000	Strong transcription	Fetal Thymus	thymus
21	chr11:74322200-74334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:74322200-74357400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:74322400-74334000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:74322600-74332400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:74322600-74332800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:74322600-74334000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:74322600-74334000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:74322600-74334200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:74322800-74332800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:74322800-74334000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:74322800-74334200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:74323000-74332800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:74323000-74332800	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:74323000-74342000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:74323000-74356800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:74323200-74337000	Weak transcription	NHLF	lung
37	chr11:74323400-74332800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr11:74323400-74332800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:74323400-74334000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr11:74323600-74333000	Strong transcription	Primary T cells from cord blood	blood
41	chr11:74324000-74345600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:74324200-74345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:74324400-74346600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:74324800-74344600	Weak transcription	NH-A	brain
45	chr11:74325000-74342200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:74325000-74345400	Weak transcription	Brain Angular Gyrus	brain
47	chr11:74325000-74345600	Weak transcription	Spleen	Spleen
48	chr11:74325000-74346400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:74325000-74351600	Weak transcription	Right Ventricle	heart
50	chr11:74325200-74347000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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