Variant report

Variant	rs1125609
Chromosome Location	chr11:74546905-74546906
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	POLR2A	chr11:74546560-74547054	K562	blood:	n/a	n/a
2	POLR2A	chr11:74546604-74547207	Hela-S3	cervix:	n/a	n/a
3	USF2	chr11:74546758-74546991	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RNF169	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs100087	0.89[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs10899043	0.84[ASN][1000 genomes]
rs11236255	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs113187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11827626	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12223829	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1282668	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1282675	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1282677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1315265	0.93[ASN][1000 genomes]
rs1315299	0.92[ASN][1000 genomes]
rs1821352	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866562	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2436762	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2510692	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132738	0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3132908	0.84[ASN][1000 genomes]
rs474431	0.84[ASN][1000 genomes]
rs474445	0.96[ASN][1000 genomes]
rs474970	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs476040	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs483271	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs487207	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487226	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs491826	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs493001	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap]
rs493889	0.94[ASN][1000 genomes]
rs494474	0.82[CEU][hapmap]
rs4944962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs496698	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs498527	0.84[ASN][1000 genomes]
rs500827	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs503855	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs503994	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs504970	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs507247	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs507620	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs512782	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs513157	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs514534	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs515429	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs516287	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs517035	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs517666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs517939	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524187	0.84[ASN][1000 genomes]
rs525802	0.84[ASN][1000 genomes]
rs527099	0.84[ASN][1000 genomes]
rs527661	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs528800	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs529186	0.84[ASN][1000 genomes]
rs532952	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs534595	0.96[ASN][1000 genomes]
rs535705	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535794	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs536823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs544852	0.84[ASN][1000 genomes]
rs544891	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs545202	0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs545304	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs548106	0.84[ASN][1000 genomes]
rs550909	0.84[ASN][1000 genomes]
rs556908	0.84[ASN][1000 genomes]
rs556916	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs557804	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs558303	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559211	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563473	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs564229	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs571250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs571437	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575064	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs575886	0.85[ASN][1000 genomes]
rs576661	0.83[ASN][1000 genomes]
rs578477	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs579581	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs580042	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs580299	0.84[ASN][1000 genomes]
rs580541	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592045	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629191	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap]
rs633824	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650130	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs655488	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs662062	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs670246	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs671544	0.87[JPT][hapmap]
rs673731	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681566	0.87[JPT][hapmap]
rs693212	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7121530	0.83[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	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
2	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
3	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
4	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1125609	XRRA1	cis	cerebellum	SCAN
rs1125609	XRRA1	cis	parietal	SCAN
rs1125609	FCHSD2	cis	cerebellum	SCAN
rs1125609	NEU3	cis	parietal	SCAN
rs1125609	PAAF1	cis	cerebellum	SCAN
rs1125609	XRRA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74533800-74553200	Weak transcription	Fetal Heart	heart
3	chr11:74538400-74553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74538400-74559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:74538400-74560000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:74538600-74554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:74539200-74557200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:74540000-74548600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:74541000-74550000	Strong transcription	Primary B cells from cord blood	blood
10	chr11:74541600-74549800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:74541600-74551400	Strong transcription	Primary T cells from cord blood	blood
12	chr11:74541800-74556400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr11:74542400-74549400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:74543600-74548400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:74543800-74549800	Strong transcription	Liver	Liver
16	chr11:74543800-74550000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:74543800-74550800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:74544000-74549800	Strong transcription	Adipose Nuclei	Adipose
20	chr11:74544000-74550600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:74544000-74557400	Strong transcription	Dnd41	blood
22	chr11:74544000-74557600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:74544200-74548800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:74544200-74549600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:74544200-74549800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:74544200-74550200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr11:74544200-74550400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr11:74544200-74557200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:74544200-74558400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:74544400-74548000	Strong transcription	HSMM	muscle
32	chr11:74544400-74549400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr11:74544600-74547600	Strong transcription	NHEK	skin
34	chr11:74544600-74550800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:74544600-74550800	Strong transcription	NH-A	brain
36	chr11:74544800-74549800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:74544800-74549800	Strong transcription	Placenta	Placenta
38	chr11:74544800-74551800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:74545000-74548000	Strong transcription	NHDF-Ad	bronchial
40	chr11:74545000-74549400	Weak transcription	Right Atrium	heart
41	chr11:74545000-74549600	Strong transcription	GM12878-XiMat	blood
42	chr11:74545000-74551200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:74545200-74548200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr11:74545200-74549400	Strong transcription	Osteobl	bone
45	chr11:74545200-74549800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:74545200-74549800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:74545200-74549800	Strong transcription	HepG2	liver
48	chr11:74545200-74551000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:74545200-74556800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr11:74545400-74549600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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