Variant report

Variant	rs2511470
Chromosome Location	chr11:67910783-67910784
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67910431..67914076-chr11:67923227..67925400,4	K562	blood:
2	chr11:67909537..67912529-chr11:67915738..67917856,2	K562	blood:
3	chr11:67900826..67903495-chr11:67908727..67910811,2	K562	blood:
4	chr11:67908238..67910865-chr11:67914661..67917297,2	MCF-7	breast:
5	chr11:67887330..67890374-chr11:67908714..67912582,4	MCF-7	breast:
6	chr11:67900826..67903728-chr11:67908566..67910811,2	K562	blood:

Variant related genes	Relation type
ENSG00000255236	Chromatin interaction
ENSG00000110721	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10791957	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs10896295	0.84[ASN][1000 genomes]
rs10896298	0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs11228129	0.87[EUR][1000 genomes]
rs11228131	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11228137	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11228144	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11228145	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11824199	0.84[EUR][1000 genomes]
rs1894204	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs2457179	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs2457180	0.80[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs2511437	0.88[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2511467	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2511468	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511469	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511472	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511473	0.93[ASN][1000 genomes]
rs2511475	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2511478	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2511479	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2512611	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs2512612	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2512623	0.86[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2512624	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133327	0.87[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes]
rs3819255	0.84[CEU][hapmap]
rs3935460	0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs4073551	0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs4345973	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs4930228	0.82[ASN][1000 genomes]
rs4930557	0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs4930561	0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs6591331	0.88[CEU][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6591333	0.82[ASN][1000 genomes]
rs7124058	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7928739	0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs7931502	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs7940113	0.84[ASN][1000 genomes]
rs7940501	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs7944372	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2511470	SPDYC	cis	parietal	SCAN
rs2511470	SF1	cis	parietal	SCAN
rs2511470	FGF19	cis	parietal	SCAN
rs2511470	PACS1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67899000-67912200	Weak transcription	Hela-S3	cervix
2	chr11:67906000-67912600	Weak transcription	Ovary	ovary
3	chr11:67906000-67912800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:67906000-67912800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:67906400-67912200	Weak transcription	A549	lung
6	chr11:67907200-67911000	Enhancers	Primary hematopoietic stem cells	blood
7	chr11:67907400-67911000	Enhancers	Pancreas	Pancrea
8	chr11:67907600-67910800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:67908000-67910800	Enhancers	Stomach Mucosa	stomach
10	chr11:67908000-67911000	Enhancers	HepG2	liver
11	chr11:67908200-67910800	Enhancers	Liver	Liver
12	chr11:67908200-67910800	Enhancers	Fetal Thymus	thymus
13	chr11:67908200-67910800	Enhancers	Gastric	stomach
14	chr11:67908200-67910800	Enhancers	Dnd41	blood
15	chr11:67908200-67912200	Weak transcription	K562	blood
16	chr11:67908400-67912200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:67908400-67912400	Weak transcription	Fetal Intestine Small	intestine
18	chr11:67908400-67912600	Weak transcription	Fetal Heart	heart
19	chr11:67908600-67910800	Enhancers	Esophagus	oesophagus
20	chr11:67908800-67910800	Enhancers	Lung	lung
21	chr11:67908800-67912600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:67908800-67914000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:67909000-67913800	Weak transcription	Fetal Lung	lung
24	chr11:67909600-67910800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr11:67909600-67913200	Weak transcription	Adipose Nuclei	Adipose
26	chr11:67909600-67913600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:67909600-67913800	Weak transcription	Brain Substantia Nigra	brain
28	chr11:67909800-67910800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:67909800-67913600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:67909800-67913800	Weak transcription	Brain Anterior Caudate	brain
31	chr11:67910000-67911000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:67910000-67912600	Weak transcription	Left Ventricle	heart
33	chr11:67910000-67913200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:67910000-67913800	Weak transcription	Brain Germinal Matrix	brain
35	chr11:67910000-67913800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:67910000-67914200	Weak transcription	Brain Angular Gyrus	brain
37	chr11:67910000-67914400	Weak transcription	HSMMtube	muscle
38	chr11:67910000-67918000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr11:67910000-67921200	Weak transcription	Primary B cells from cord blood	blood
40	chr11:67910200-67912000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:67910200-67912000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:67910200-67912600	Weak transcription	Right Ventricle	heart
43	chr11:67910200-67913600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:67910200-67913800	Weak transcription	Colonic Mucosa	Colon
45	chr11:67910400-67911000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr11:67910400-67911200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr11:67910400-67912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:67910400-67912600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:67910400-67913800	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:67910400-67913800	Weak transcription	HMEC	breast

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