Variant report

Variant	rs571250
Chromosome Location	chr11:74465068-74465069
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	CEBPB	chr11:74465046-74465246	A549	lung:	n/a	chr11:74465141-74465152
2	STAT3	chr11:74465052-74465252	MCF10A-Er-Src	breast:	n/a	chr11:74465125-74465133
3	CHD1	chr11:74464504-74467374	IMR90	lung:	n/a	n/a
4	CEBPB	chr11:74465054-74465225	HepG2	liver:	n/a	chr11:74465141-74465152

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74457724..74462703-chr11:74463031..74468958,12	K562	blood:
2	chr11:74441741..74443246-chr11:74464573..74467415,2	K562	blood:

Variant related genes	Relation type
ENSG00000264095	TF binding region
ENSG00000166439	Chromatin interaction
ENSG00000054938	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs100087	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10899043	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236243	0.84[ASN][1000 genomes]
rs11236255	0.84[ASN][1000 genomes]
rs1125609	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]
rs113187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11827626	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12223829	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1282668	0.85[EUR][1000 genomes]
rs1282675	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1282677	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1315265	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1315299	0.81[ASN][1000 genomes]
rs1821352	0.84[ASN][1000 genomes]
rs1866562	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2436762	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510692	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132738	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132908	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474431	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474445	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474970	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476040	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs483271	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487207	0.84[ASN][1000 genomes]
rs487226	0.82[EUR][1000 genomes]
rs491826	0.81[ASN][1000 genomes]
rs493889	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs496698	0.82[EUR][1000 genomes]
rs498527	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500827	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs503855	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs503994	0.84[EUR][1000 genomes]
rs504970	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs507247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507620	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512782	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513157	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs514534	0.82[EUR][1000 genomes]
rs515429	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs516287	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs517035	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs517939	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524187	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs525802	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs527099	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs527661	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs528800	0.80[EUR][1000 genomes]
rs529186	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532952	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533220	0.94[ASN][1000 genomes]
rs534595	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs535705	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs535794	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536823	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544852	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544891	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs545202	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs545304	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs548106	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs550909	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556908	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556916	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs557804	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558303	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559211	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs563473	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564229	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571437	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs575064	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs575886	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576661	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578477	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs579581	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs580042	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs580299	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs580541	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592045	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59735998	0.80[ASN][1000 genomes]
rs605954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629191	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs633824	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650130	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs655488	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs662062	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs673731	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs693212	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7121530	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	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
7	esv1840811	chr11:74452658-74488369	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs571250	XRRA1	cis	parietal	SCAN
rs571250	NEU3	cis	parietal	SCAN
rs571250	OR9A2	trans	cerebellum	SCAN
rs571250	XRRA1	cis	lymphoblastoid	seeQTL
rs571250	PAAF1	cis	cerebellum	SCAN
rs571250	FCHSD2	cis	cerebellum	SCAN
rs571250	XRRA1	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74461200-74465600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:74461200-74465600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:74461200-74465600	Weak transcription	Gastric	stomach
4	chr11:74461200-74465600	Weak transcription	Left Ventricle	heart
5	chr11:74461200-74465600	Weak transcription	Small Intestine	intestine
6	chr11:74461200-74465800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:74461200-74465800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:74461200-74466000	Weak transcription	Fetal Kidney	kidney
9	chr11:74461200-74466200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:74461200-74466600	Weak transcription	Right Ventricle	heart
11	chr11:74461200-74479400	Weak transcription	Spleen	Spleen
12	chr11:74461400-74465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:74461400-74465200	Weak transcription	Brain Anterior Caudate	brain
14	chr11:74461400-74465800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:74461400-74465800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:74461400-74465800	Weak transcription	Stomach Mucosa	stomach
17	chr11:74461600-74465200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:74461600-74465600	Weak transcription	Right Atrium	heart
19	chr11:74461600-74465800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:74461600-74465800	Weak transcription	Brain Angular Gyrus	brain
21	chr11:74461600-74465800	Weak transcription	Brain Hippocampus Middle	brain
22	chr11:74461600-74465800	Weak transcription	HSMMtube	muscle
23	chr11:74461600-74466400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:74461600-74466600	Weak transcription	Psoas Muscle	Psoas
25	chr11:74461600-74467000	Weak transcription	Lung	lung
26	chr11:74461600-74467600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:74461600-74473600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:74461600-74474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:74461600-74475000	Weak transcription	Fetal Intestine Small	intestine
30	chr11:74461600-74476400	Weak transcription	Thymus	Thymus
31	chr11:74461600-74494000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:74461800-74465800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:74462000-74466600	Weak transcription	Placenta	Placenta
34	chr11:74462000-74470200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:74462200-74465600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:74462200-74465600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:74462200-74465600	Weak transcription	Esophagus	oesophagus
38	chr11:74462200-74465600	Weak transcription	Ovary	ovary
39	chr11:74462200-74465600	Weak transcription	Pancreas	Pancrea
40	chr11:74462200-74466400	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:74462200-74474800	Weak transcription	Fetal Stomach	stomach
42	chr11:74462400-74465400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr11:74462400-74465600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:74462400-74465800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:74462400-74466400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr11:74462400-74479000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:74462400-74481200	Weak transcription	Primary T cells from cord blood	blood
48	chr11:74462600-74465400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:74462600-74465600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr11:74462600-74465600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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